The 9+2 axoneme structure of the motile flagellum/cilium is an iconic, apparently symmetrical cellular structure. Recently, asymmetries along the length of motile flagella have been identified in a number of organisms, typically in the inner and outer dynein arms. Flagellum beat waveforms are adapted for different functions. They may start either near the flagellar tip or near its base (and may be symmetrical or asymmetrical. We hypothesised that proximal/distal asymmetry in the molecular composition of the axoneme may control the site of waveform initiation and direction of waveform propagation. The unicellular eukaryotic pathogens Trypanosoma brucei and Leishmania mexicana often switch between tip-to-base and base-to-tip waveforms, making them ideal for analysis of this phenomenon. We show here that the proximal and distal portions of the flagellum contain distinct outer dynein arm docking complex heterodimers. This proximal/distal asymmetry is produced and maintained through growth by a concentration gradient of the proximal docking complex, generated by intraflagellar transport. Furthermore, this asymmetry is involved in regulating whether a tip-tobase or base-to-tip beat occurs, which is linked to a calcium-dependent switch. Our data show that the mechanism for generating proximal/distal flagellar asymmetry can control waveform initiation and propagation direction. Significance statementThe motile flagellum/cilium is found across all eukaryotic life, and it performs critical functions in many organisms including humans. A fundamental requirement for a motile flagellum/cilium is that it must undergo the correct and appropriate waveform for its specific function. Much is known about the generation of asymmetry in flagellum movement, however it is unknown how a motile flagellum specifies where waves should start and whether waves should go from base-to-tip, or from tip-tobase. We show here that in two flagellum model organisms (the human parasites Trypanosoma brucei and Leishmania mexicana, differences in the outer dynein arms between the distal and proximal regions of the flagellum determine wave propagation direction, and are generated and maintained by the flagellum growth machinery.