Cilia and flagella share fundamentally identical internal architecture termed axoneme composed of nine peripheral microtubule doublets surrounding two central singlets, 9+2 arrangement, radial spokes, and dynein motor arms producing bending via ATP hydrolysis and basal body anchoring. Ultrastructurally and proteomically they are synonymous organelles using tubulin and intraflagellar transport. Distinction rests on length, quantity, and waveform: flagella typically longer, fewer, propelling with undulating waves, while cilia are shorter, numerous, beating coordinately in metachronal waves to move fluids or cells, not internal microtubule composition.
Ref:
Campbell Biology 11th ed., Chapter 6 Cilia flagella length number waveform same ultrastructure; Cooper Cell Biology 9+2 axoneme