How flagellar length regulation is achieved in multiciliated eukaryotic cells with flagella of different equilibrium lengths is unknown. The protist
Giardia lambliais an ideal model to evaluate length regulation as it has flagella of four different lengths. Giardiaaxonemes have both non-membrane-bound and membrane-bound regions, but lack transition zones. Here we quantified the contributions of intraflagellar transport (IFT)-mediated assembly and kinesin-13-mediated disassembly to length control. IFT particles assemble and inject at Giardia’sflagellar pore complexes, which act as diffusion barriers functionally analogous to the transition zone to compartmentalize the membrane-bound regions of flagella. IFT-mediated assembly is length-independent as train size, speed, and injection frequencies are similar between flagella of different lengths. In Giardia, kinesin-13 mediates a length-dependent disassembly mechanism of length regulation to balance length-independent IFT-mediated assembly, resulting in different lengths. We anticipate that similar control mechanisms are widespread in multiciliated cells where cytoplasmic precursor pools are not limiting.