Abstract Flagella are highly conserved organelles comprised of several hundred proteins that are assembled using the equally conserved mechanism called intraflagellar transport (IFT). The molecular motors dynein and kinesin drive IFT‐mediated flagellar assembly. In addition, flagellar movement is powered by the flagellar dynein motors. The outer and inner dynein arms function in generating flagellar beat frequency and flagellar waveform that are the two main features of flagellar bending. The biflagellate algae Chlamydomonas reinhardtii is a powerful model organism for the study of flagellar assembly and function. Recent advances have revealed that cilia and flagella play vital motile and sensory roles in the developing human embryo and in adult tissue function. Defects in assembly or function of mammalian cilia/flagella underlie an expanding set of human diseases and syndromes, collectively called ‘the ciliopathies’. Much of our current understanding of flagellar assembly, motility and the ciliopathies has come from studies in Chlamydomonas . Key Concepts: Cilia and flagella are highly conserved organelles. Dynein motors drive flagellar movement. Chlamydomonas reinhardtii is a powerful model experimental system for studying flagella. Defects in assembly or function of cilia/flagella result in multiple pathologies called ‘the ciliopathies’.