What is the main difference between cilia and flagella?

The main difference is length and number; cilia are short and numerous, covering the cell surface, while flagella are long and few, typically one or two per cell.

Which is better for moving a whole cell, cilia or flagella?

Flagella are better for moving a whole cell because their long, whip-like structure generates thrust to propel sperm or bacteria forward efficiently.

What is the cost difference in energy use between cilia and flagella?

Flagella generally cost less energy per beat because their fewer, longer structures move larger volumes of fluid with less frequent ATP hydrolysis than many cilia.

Are there safety risks when cilia or flagella malfunction?

Yes, malfunctioning cilia risk respiratory infections and infertility, while defective flagella risk male infertility, because both impair essential fluid and cell movement.

Are cilia and flagella compatible in the same organism?

Yes, cilia and flagella are compatible in the same organism, as seen in the human body where respiratory cilia and sperm flagella coexist in different tissues.

What is a common beginner mistake when studying cilia and flagella?

A common beginner mistake is assuming cilia only move cells, when they also move fluids past stationary cells, such as mucus in airways.

Are cilia and flagella interchangeable in function?

No, cilia and flagella are not interchangeable because their distinct lengths and numbers suit different tasks, like sweeping versus propulsion.

What is a real-world use case for cilia in the human body?

A real-world use case for cilia is clearing mucus and trapped particles from the lungs, a process called mucociliary clearance that prevents infection.

Can I switch from using flagella to cilia for cell movement?

No, you cannot switch from flagella to cilia for cell movement because the core structure is fixed by genetics, determining which organelle a cell type develops.

How do cilia and flagella differ in their internal structure?

Cilia and flagella share the same internal structure, a 9+2 microtubule arrangement, but differ only in length, number, and beating pattern.

Difference Between

Difference Between Cilia and Flagella

Written byNex Virox Team

Editorial Team

Reviewed byVarshal Nirbhavane

Senior SEO & Organic Growth Professional · 5+ years

Published: September 6, 202618 min read

Quick answer

The main difference between Cilia and Flagella is that Cilia are short, numerous hair-like projections that beat in coordinated waves, while Flagella are long, few whip-like tails that propel with a wave-like motion. Cilia is a short, hair-like organelle moving substances across cell surfaces, while Flagella is a long, whip-like organelle moving entire cells.

Key takeaways

Core distinction: Cilia are short, numerous, and move in coordinated oar-like strokes, while flagella are long, few, and wave.
How each works: Cilia beat synchronously to move fluids across cell surfaces, whereas flagella propel entire cells through liquid environments.
Performance metrics: Cilia typically measure 5-10 micrometers long, but flagella reach 150 micrometers, making flagella significantly longer structures.
Best-fit use case: Cilia line respiratory airways to clear mucus, while flagella power sperm cells and single-celled organisms like Euglena.
Common decision mistake: Confusing primary cilia with motile cilia; primary cilia sense signals while motile cilia create movement, unlike flagella.

Table of Contents18 sections

Difference Between Cilia and Flagella: Comparison Table

Aspect	Cilia	Flagella
Definition	Short, hair-like organelles projecting from cell surfaces, typically present in large numbers.	Long, whip-like organelles, usually one to a few per cell, used for propulsion.
Primary Purpose	Move fluids across cell surfaces or propel single cells through liquid environments.	Propel entire cells, such as sperm or bacteria, through liquid media.
Core Mechanism	Beat in a coordinated, back-and-forth power stroke followed by a recovery stroke.	Undulate in a wave-like pattern, either planar or helical, to generate thrust.
Length	Short, typically 5 to 10 micrometers in length across most eukaryotic cells.	Long, typically 150 micrometers in length, often exceeding the cell body size.
Diameter	Thicker, with a diameter around 0.25 micrometers along the entire shaft.	Thinner, with a diameter around 0.2 micrometers, similar to cilia width.
Number Per Cell	Numerous, with hundreds to thousands covering a single cell surface area.	Few, usually one to four flagella per cell, depending on the organism type.
Arrangement	Distributed across the entire cell surface in dense, uniform patterns.	Located at one pole or scattered, often at the posterior or anterior end.
Beat Pattern	Oar-like, with a stiff power stroke and a flexible, curling recovery stroke.	Sinusoidal or helical undulation that propagates from base to tip continuously.
Movement Type	Coordinated, metachronal rhythm creates a wave across the cell surface.	Independent, autonomous beating that drives the cell forward or changes direction.
Speed	Beat rapidly, often at frequencies of 10 to 40 beats per second in mammals.	Rotate or undulate at rates that vary widely, often 10 to 40 cycles per second.
Force Generation	Generate force parallel to the cell surface to move extracellular fluid.	Generate force parallel to the flagellum axis to push the cell body forward.
Energy Source	Powered by ATP hydrolysis from dynein motor proteins along microtubules.	Powered by ATP hydrolysis, or proton motive force in bacterial flagella.
Microtubule Structure	Contain a 9+2 arrangement of microtubules in most eukaryotic cilia.	Contain a 9+2 arrangement in eukaryotes, but a single microtubule in bacteria.
Dynein Arms	Inner and outer dynein arms drive sliding between adjacent microtubule pairs.	Dynein arms are present in eukaryotic flagella, but absent in bacterial versions.
Basal Body	Anchored at a basal body derived from a centriole at the cell cortex.	Anchored at a basal body, which is structurally identical to a centriole.
Covering Membrane	Covered by the plasma membrane, continuous with the cell's outer membrane.	Covered by the plasma membrane in eukaryotes, but not in bacterial flagella.
Rotation Capability	Do not rotate; they only bend and flex through their beat cycle.	Bacterial flagella rotate like a propeller at the base, not just bend.
Reversibility	Can reverse beat direction to alter fluid flow or cell movement.	Can reverse rotation direction to change swimming path or back up.
Coordination	Beat in a highly coordinated, metachronal wave across the entire surface.	Beat independently, though multiple flagella may synchronize in some species.
Permanence	Often permanent structures, though some can be resorbed during cell division.	Often permanent, but some bacteria shed flagella under certain conditions.
Assembly Cost	High energy cost to build hundreds of complex microtubule-based shafts.	Lower total cost per cell, as only a few flagella are constructed.
Maintenance	Require constant intraflagellar transport to maintain shaft length and function.	Require intraflagellar transport in eukaryotes, but self-assemble in bacteria.
Regeneration	Can regenerate fully after amputation, typically within a few hours.	Can regenerate after loss, though speed depends on the organism and type.
Sensory Function	Act as sensory antennae, detecting chemical, mechanical, or light signals.	Primarily motor, but some flagella also sense environmental chemical gradients.
Examples	Line the human respiratory tract to move mucus and trap inhaled particles.	Drive sperm cells in humans and many animals toward the egg for fertilization.
Non-Motile Variants	Primary cilia are non-motile and serve as cellular signaling hubs.	No common non-motile flagella; they are almost exclusively motile structures.
Organism Range	Found in protozoans, invertebrates, and vertebrates, but not in bacteria.	Found in bacteria, archaea, protozoans, algae, and animal sperm cells.
Evolutionary Origin	Evolved from ancestral flagella, then adapted for surface fluid movement.	Evolved early in eukaryotes, with bacterial flagella arising independently.
Dysfunction Impact	Defects cause primary ciliary dyskinesia, leading to chronic respiratory infections.	Defects cause sperm immotility, contributing directly to male infertility.
Best-Fit Scenario	Best for moving fluid over a fixed surface, like clearing mucus from airways.	Best for free-swimming locomotion, like a sperm cell navigating to an egg.

What Is Cilia?

Cilia are tiny, hair-like organelles extending from the surface of many eukaryotic cells. They beat in coordinated waves to move fluid across tissues or propel single cells through liquid environments. Cilia exist to perform essential tasks such as clearing mucus, moving eggs, and sensing extracellular signals.

Definition of Cilia

Cilia are microtubule-based, membrane-bound projections anchored by a basal body, typically 5-10 micrometers long and 0.2 micrometers wide. They contain a characteristic 9+2 axoneme arrangement of microtubules. Their primary functions include generating directed fluid flow, facilitating cell motility, and mediating mechanosensory or chemosensory signal transduction in diverse organisms.

Key Characteristics of Cilia

Characteristic	What It Means in Practice
Microtubule core	Nine outer doublet microtubules drive bending; the axoneme provides structural rigidity and shape.
Basal body anchor	A centriole-derived structure at the base fixes the cilium and organises its microtubule assembly.
Beat pattern	Coordinated whip-like strokes create a power stroke and a recovery stroke to move fluid directionally.
Membrane covering	A continuous plasma membrane encloses the axoneme, hosting receptors for sensing external chemical or mechanical cues.
Dynein motor arms	ATP-powered dynein proteins slide adjacent microtubules, converting chemical energy into bending force.
Length range	Typically 5-10 micrometers long, making them shorter and more numerous than flagella on the same cell.
High density	Hundreds to thousands can cover one cell surface, enabling broad, coordinated sweeping action.
Coordinated beating	Adjacent cilia beat in metachronal waves, creating efficient, unidirectional fluid transport.
Two functional types	Motile cilia move fluid; primary cilia act as sensory antennae without beating.
Dynamic assembly	Intraflagellar transport builds and maintains the structure, allowing rapid repair or resorption.

Common Examples of Cilia

Respiratory epithelial cilia – line airways and sweep mucus-trapped dust and pathogens upward toward the throat.
Fallopian tube cilia – beat to transport the released ovum from the ovary toward the uterus.
Paramecium cilia – cover this single-celled organism entirely, enabling rapid swimming and food capture.
Ependymal cell cilia – line brain ventricles and circulate cerebrospinal fluid around the central nervous system.
Primary cilia on kidney tubules – act as flow sensors that detect urine movement and regulate cell signalling.
Olfactory receptor cilia – extend from nasal neurons and house odorant receptors for smell detection.
Photoreceptor connecting cilia – link inner and outer segments of retinal rods and cones, transporting proteins.
Embryonic node cilia – generate leftward fluid flow that establishes left-right body asymmetry during development.
Tracheal cilia in insects – line respiratory tubes and help move air or fluid through the tracheal system.
Gill cilia of bivalves – create water currents that bring in food particles and oxygen for filter feeding.

Advantages and Limitations of Cilia

Advantages	Limitations
Highly efficient fluid transport over large epithelial surfaces	Requires continuous ATP supply, making cilia energetically expensive to maintain and beat.
Precise directional control via coordinated metachronal wave patterns	Beating stops or becomes uncoordinated if mucus viscosity rises abnormally, as in cystic fibrosis.
Dual roles in motility and sensory detection within one structure	Primary cilia lack motor proteins, so they cannot move fluid or propel cells at all.
Rapid assembly and disassembly allows quick response to environmental changes	Structural defects in dynein arms cause immotile cilia syndrome with severe respiratory consequences.
Numerous cilia per cell multiply force output for strong sweeping action	High density increases membrane surface area, raising susceptibility to pathogen attachment.
Works in low-Reynolds-number environments where viscosity dominates	Cannot function effectively in air; cilia require a liquid or mucus layer to beat against.
Enables single-cell organisms to hunt, escape predators, and feed	Length is fixed; cilia cannot grow longer to handle larger particles or faster flow.
Sensory cilia detect mechanical, chemical, and optical signals	Loss of primary cilia disrupts signalling pathways, contributing to polycystic kidney disease.
Self-repairing through intraflagellar transport mechanisms	Repair is slow; damaged cilia take hours to regenerate, leaving cells vulnerable.
Conserved across eukaryotes, indicating ancient evolutionary success	Any genetic mutation in assembly proteins leads to broad, multi-organ ciliopathy disorders.

What Is Flagella?

Flagella are long, whip-like appendages that protrude from the cell surface and provide propulsion. They rotate or undulate to move cells through liquid environments, enabling essential functions like finding nutrients, escaping toxins, and reaching host cells for infection.

Definition of Flagella

Flagella are slender, thread-like organelles composed of microtubules or protein filaments that extend from the cell body. They generate motility through a basal body-driven rotational or bending mechanism, allowing unicellular organisms and certain cell types to swim effectively in aqueous media.

Key Characteristics of Flagella

Characteristic	What It Means in Practice
Length	Flagella are typically 10 to 15 micrometers long, extending well beyond the cell body diameter.
Whip-like motion	They generate propulsion through a sinusoidal or rotational wave that pushes against the surrounding fluid.
Microtubule core	Eukaryotic flagella contain a 9+2 arrangement of microtubules that drives their bending movement.
Basal body anchor	A basal body at the cell membrane anchors the flagellum and acts as the motor for rotation.
Rotational motor	Bacterial flagella use a rotary motor powered by proton or sodium ion gradients to spin.
Filament structure	Bacterial flagella are made of the protein flagellin, which self-assembles into a hollow helix.
Low number per cell	Most flagellated cells carry one to eight flagella, unlike the dense coverage seen on ciliated surfaces.
Directional control	Cells can reverse flagellar rotation to change swimming direction, enabling chemotaxis toward attractants.
Energy consumption	Flagellar movement consumes ATP in eukaryotes or ion gradients in bacteria to sustain motion.
Universal distribution	Flagella appear across bacteria, archaea, and eukaryotes, showing remarkable structural diversity.

Common Examples of Flagella

Escherichia coli – a bacterium with 4-10 peritrichous flagella that bundle to swim through the gut.
Trypanosoma brucei – a parasite with a single flagellum that drives movement in blood and tissues.
Sperm cells – human and animal sperm use one long flagellum to propel toward the egg.
Salmonella enterica – a pathogen whose flagella enable invasion of intestinal epithelial cells.
Chlamydomonas reinhardtii – a green alga with two flagella used for both swimming and mating.
Vibrio cholerae – a curved bacterium with a single polar flagellum that powers rapid swimming.
Pseudomonas aeruginosa – an opportunistic pathogen using polar flagella for surface attachment and spread.
Euglena gracilis – a single-celled alga whose flagellum helps it navigate toward light.
Helicobacter pylori – a stomach pathogen with multiple sheathed flagella that bore through mucus.
Archaeal flagella – structurally distinct from bacterial versions yet still enable swimming in extreme environments.

Advantages and Limitations of Flagella

Advantages	Limitations
Enables rapid locomotion toward nutrients and away from harmful chemicals.	Flagella are energetically expensive to assemble and rotate continuously.
Provides high swimming speeds, reaching up to 60 cell lengths per second.	Function is lost in viscous or thick environments where beating becomes ineffective.
Allows precise chemotaxis by reversing rotation to reorient direction.	Flagellin protein triggers strong host immune responses during bacterial infection.
Facilitates biofilm formation by helping cells reach and adhere to surfaces.	Flagella are fragile and shear off easily under mechanical stress or high flow.
Enables host colonisation for pathogens, increasing infectivity.	Structural complexity demands many genes, creating a high metabolic burden.
Provides a sensitive environmental sensor for detecting chemical gradients.	Loss of flagella can cripple motility-dependent survival strategies.
Works across diverse species, from archaea to mammalian sperm.	Eukaryotic flagella are permanently anchored and cannot be retracted.
Allows rapid escape from predators or hostile microenvironments.	Bacterial flagella rotation is inhibited by high external viscosity.
Enables fertilisation by powering sperm migration through reproductive tracts.	Flagellar assembly requires precise protein export machinery that is easily disrupted.
Supports dispersal to new niches, aiding population survival.	Immune systems can target flagellin to neutralise motile pathogens.

Similarities Between Cilia and Flagella

Shared Aspect	How Cilia and Flagella Are Alike
Core function	Cilia and flagella both generate controlled movement that propels cells or moves fluid over cell surfaces.
Basic structure	Cilia and flagella both extend from the cell surface as hair-like projections enclosed by a plasma membrane.
Microtubule core	Cilia and flagella both contain a structural core of microtubules arranged in a characteristic pattern.
9+2 arrangement	Cilia and flagella both typically share the nine peripheral doublet microtubules with two central singlet microtubules.
Basal body	Cilia and flagella both anchor to the cell at a basal body derived from a centriole.
Dynein motors	Cilia and flagella both rely on the motor protein dynein to power their bending motion.
ATP energy	Cilia and flagella both consume adenosine triphosphate as the direct chemical energy source for movement.
Sliding mechanism	Cilia and flagella both bend when dynein arms cause adjacent microtubule doublets to slide past each other.
Eukaryotic presence	Cilia and flagella both occur in eukaryotic organisms ranging from single-celled protists to complex animals.
Evolutionary origin	Cilia and flagella both share an ancient evolutionary origin from a common ancestral microtubule-based structure.
Assembly process	Cilia and flagella both assemble through intraflagellar transport that delivers building materials to their tips.
Intraflagellar transport	Cilia and flagella both depend on the bidirectional movement of protein cargo along their microtubule tracks.
Membrane continuity	Cilia and flagella both maintain a continuous membrane with the cell body, allowing signal exchange.
Receptor function	Cilia and flagella both serve as sensory antennae that detect chemical and mechanical signals from the environment.
Signaling hub	Cilia and flagella both concentrate receptors and signaling molecules to mediate cellular response pathways.
Cell motility	Cilia and flagella both enable whole-cell locomotion in free-living organisms like sperm and algae.
Fluid movement	Cilia and flagella both create directed fluid currents across epithelial surfaces in respiratory and reproductive tracts.
Beat pattern	Cilia and flagella both exhibit rhythmic, coordinated beating cycles that alternate between power and recovery strokes.
Structural polarity	Cilia and flagella both display a defined longitudinal polarity with distinct proximal and distal regions.
Dynamic instability	Cilia and flagella both undergo continuous assembly and disassembly of tubulin at their distal tips.
Genetic control	Cilia and flagella both require hundreds of shared genes that encode structural and regulatory proteins.
Defect sensitivity	Cilia and flagella both suffer impaired function when dynein or microtubule genes carry mutations.
Disease link	Cilia and flagella both contribute to ciliopathies when their assembly or motility is disrupted.
Primary immotile	Cilia and flagella both have non-motile variants that retain sensory and signaling functions.
Length regulation	Cilia and flagella both tightly regulate their length through balanced assembly and disassembly rates.
Temperature sensitivity	Cilia and flagella both show reduced beating activity when environmental temperature drops significantly.
Viscosity response	Cilia and flagella both adjust their beat frequency in response to changes in surrounding fluid viscosity.
Calcium role	Cilia and flagella both use intracellular calcium ions to modulate their beating direction and frequency.
Pharmacological target	Cilia and flagella both respond to inhibitors like colchicine that disrupt microtubule polymerization.
Research utility	Cilia and flagella both serve as model systems for studying microtubule dynamics and motor protein mechanics.

Cilia or Flagella: Which Should You Choose?

The deciding variable is how many appendages you need and how they must move. Choose Cilia for many short, synchronized oars that sweep fluids across a surface. Choose Flagella for one or a few long, whip-like motors that propel an entire cell forward.

When to Use Cilia

Choose Cilia when you need many short appendages covering a surface to move fluid or particles. Use them for sweeping mucus in airways, moving eggs in fallopian tubes, or creating feeding currents in small organisms. They suit tasks requiring precise, coordinated, back-and-forth strokes.

When to Use Flagella

Choose Flagella when you need one or two long appendages to propel a whole cell through liquid. Use them for sperm swimming, bacterial motility, or moving through viscous environments. They suit tasks requiring fast, independent, undulating movement rather than surface-level sweeping.

Common Misconceptions About Cilia and Flagella

Common Myth	The Reality
Cilia are always shorter than flagella on every cell.	Cilia are typically shorter, but flagella can be short too; length alone never reliably distinguishes the two structures.
Flagella only exist on sperm cells in humans.	Flagella also appear on other human cells, yet sperm is the only free-swimming human cell using one.
Cilia always move in a coordinated, wave-like rhythm.	Motile cilia beat in coordinated waves, but primary cilia are immotile and serve sensory functions instead.
All cilia and flagella have the same internal structure.	Both share a 9+2 microtubule arrangement, but primary cilia lack the central pair and are non-motile.
Flagella are simply longer versions of cilia.	Flagella differ in beat pattern, length, and often number, not just in size compared to cilia.
Cilia move fluid, while flagella move the entire cell.	Both can move cells or fluids; cilia often move fluid, but flagella also propel single cells forward.
Bacteria have cilia just like human cells do.	Bacteria lack true cilia; their flagella have a different structure and rotation mechanism than eukaryotic flagella.
Flagella beat in a smooth, snake-like undulation.	Eukaryotic flagella use a whip-like or planar beat, while bacterial flagella rotate like a propeller instead.
Cilia are only found in the respiratory tract.	Cilia line the respiratory tract, but also appear in the female reproductive tract and brain ventricles.
Primary cilia are just non-functional leftovers.	Primary cilia act as cellular antennas, sensing chemical and mechanical signals critical for development.
Flagella and cilia are made of the same protein as muscle.	Both structures are built from tubulin, not actin, which is the protein found in muscle fibers.
One cell can have both cilia and flagella simultaneously.	Some single-celled organisms possess both, but most human cells have either cilia or a single flagellum.
Cilia always push particles in one direction only.	Motile cilia typically push in one direction, but some organisms reverse beat direction to change movement.
Flagella are too small to see with a light microscope.	Flagella are visible with light microscopy when stained, though their fine detail requires electron microscopy.
All cilia are covered by the same cell membrane type.	Cilia extend from the plasma membrane, but their membrane composition differs from the rest of the cell.
Flagella only help cells swim in liquid environments.	Flagella also help cells move across surfaces and sense environmental conditions, not just swim in fluids.
Cilia cannot be found on single-celled organisms.	Many single-celled organisms like Paramecium use cilia for locomotion and feeding in aquatic habitats.
Flagella always occur singly on every cell type.	Flagella can be single, paired, or multiple, depending on the organism and its specific cellular function.
Motile cilia and flagella use the same motor protein.	Both use dynein, but flagella may also use kinesin for intraflagellar transport along the axoneme.
Cilia are static structures that never change length.	Cilia undergo dynamic assembly and disassembly, changing length in response to cell cycle and signals.
Flagella are only found on prokaryotic cells like bacteria.	Flagella exist on eukaryotic cells too, including sperm, algae, and protozoa, with different structures.
Primary cilia do not contain microtubules at all.	Primary cilia contain nine outer microtubule doublets but lack the central pair found in motile cilia.
Cilia always beat faster than flagella in every organism.	Beat frequency varies widely; some flagella beat faster than cilia depending on species and function.
Flagella cannot be found on cells lining human organs.	Flagella are rare on human organ linings, but cilia are common; flagella mainly appear on sperm cells.
Cilia are only used for movement, never for sensing.	Primary cilia sense signals, and even motile cilia can detect flow, making them sensory organelles too.
Flagella and cilia both originate from the same basal body.	Both structures anchor at a basal body, but flagella often have a longer transition zone than cilia.
All flagella rotate in a clockwise direction only.	Bacterial flagella rotate both clockwise and counterclockwise to switch between running and tumbling behavior.
Cilia are completely absent from the human brain.	Primary cilia are present on neurons in the brain, where they help regulate signaling and behavior.
Flagella are always longer than the cell body itself.	Flagella can be longer than the cell, but some are shorter, especially on certain protozoa and algae.
Cilia and flagella cannot be distinguished by beat pattern.	Cilia use a back-and-forth stroke, while flagella use undulating or rotational motion, making patterns distinct.

Conclusion

Difference Between Cilia and Flagella comes down to number and motion. Cilia are many, short, and beat in coordinated strokes for movement or sensing. Flagella are few, long, and whip in waves for propulsion. Choose cilia for sweeping surfaces; choose flagella for single-cell swimming.

FAQs on Difference Between Cilia and Flagella

What is the main difference between cilia and flagella?: The main difference is length and number; cilia are short and numerous, covering the cell surface, while flagella are long and few, typically one or two per cell.
Which is better for moving a whole cell, cilia or flagella?: Flagella are better for moving a whole cell because their long, whip-like structure generates thrust to propel sperm or bacteria forward efficiently.
What is the cost difference in energy use between cilia and flagella?: Flagella generally cost less energy per beat because their fewer, longer structures move larger volumes of fluid with less frequent ATP hydrolysis than many cilia.
Are there safety risks when cilia or flagella malfunction?: Yes, malfunctioning cilia risk respiratory infections and infertility, while defective flagella risk male infertility, because both impair essential fluid and cell movement.
Are cilia and flagella compatible in the same organism?: Yes, cilia and flagella are compatible in the same organism, as seen in the human body where respiratory cilia and sperm flagella coexist in different tissues.
What is a common beginner mistake when studying cilia and flagella?: A common beginner mistake is assuming cilia only move cells, when they also move fluids past stationary cells, such as mucus in airways.
Are cilia and flagella interchangeable in function?: No, cilia and flagella are not interchangeable because their distinct lengths and numbers suit different tasks, like sweeping versus propulsion.
What is a real-world use case for cilia in the human body?: A real-world use case for cilia is clearing mucus and trapped particles from the lungs, a process called mucociliary clearance that prevents infection.
Can I switch from using flagella to cilia for cell movement?: No, you cannot switch from flagella to cilia for cell movement because the core structure is fixed by genetics, determining which organelle a cell type develops.
How do cilia and flagella differ in their internal structure?: Cilia and flagella share the same internal structure, a 9+2 microtubule arrangement, but differ only in length, number, and beating pattern.