Microtubules (MTs) interact with force-generating proteins to generate a variety of intracellular movements, including intracellular particle transport, ciliary-flagellar beating, and chromosome-spindle movements during mitosis-meiosis. Relatively little is known about the mechanics of these motor-MT interactions, in part because the motor binding domains of the MT and the corresponding MT binding domains of the motor have not been well characterized. Using a flagellar motility assay, we report that the MT subunits, alpha- and beta-tubulin, each contain a dynein binding domain located near the C-termini of their respective tubulin subunits. Blocking either alpha- or beta-tubulin binding domains of dynein attenuates motility in demembranated sea urchin sperm up to 50%. Interestingly, blocking both alpha- and beta-tubulin binding domains on dynein produces much greater decreases in motility. These data suggest that flagellar dynein binds to both subunits of the MT polymer, alpha- and beta-tublin. In addition, the two subunits appear to contribute equivalent, but functionally separate, roles to flagellar motility.