1How flagellar length regulation is achieved in multiciliated eukaryotic cells with flagella of 2 different equilibrium lengths is unknown. The protist Giardia lamblia is an ideal model to 3 evaluate length regulation as it has flagella of four different lengths. Giardia axonemes have 4 both non-membrane-bound and membrane-bound regions, but lack transition zones. Here we 5 quantified the contributions of intraflagellar transport (IFT)-mediated assembly and kinesin-13-6 mediated disassembly to length control. IFT particles assemble and inject at Giardia's flagellar 7 pore complexes, which act as diffusion barriers functionally analogous to the transition zone to 8 compartmentalize the membrane-bound regions of flagella. IFT-mediated assembly is length-9 independent as train size, speed, and injection frequencies are similar between flagella of 10 different lengths. In Giardia, kinesin-13 mediates a length-dependent disassembly mechanism 11 of length regulation to balance length-independent IFT-mediated assembly, resulting in 12 different lengths. We anticipate that similar control mechanisms are widespread in multiciliated 13 cells where cytoplasmic precursor pools are not limiting. 14 15 16 17