The organization of the flagellar apparatus of Polytomella and the pattern of flagellar movement have been described previously ( D.L. Brown, A. Massalski, and R. Patenaude, 1976, J. Cell Biol. 69, 106–125). In this study we have used an isolation and purification procedure which preserves the structural organization of the basal apparatus and permits cytochemical and biochemical analysis of ATPase activities. The basal apparatus ATPase activities differed from those of the isolated flagellar axonemes in pH and divalent cation concentration optima, substrates hydrolyzed, K m values of ATP, and in sensitivity to the ATPase inhibitor vanadate. Utilizing the optimal conditions established, ATPase and GTPase activities were cytochemically localized on several structures of the basal apparatus which have been implicated in the control of flagellar movement including the striated rootlets, fibers interconnecting the basal bodies, and in the central core of the basal body transition region.