Variations in musculoskeletal lever systems have formed an important foundation for predictions about the diversity of muscle function and organismal performance. Changes in the structure of lever systems may be coupled with changes in muscle use and give rise to novel muscle functions. The two extant turtle lineages, cryptodires and pleurodires, exhibit differences in hindlimb structure. Cryptodires possess the ancestral musculoskeletal morphology, with most hip muscles originating on the pelvic girdle, which is not fused to the shell. In contrast, pleurodires exhibit a derived morphology, in which fusion of the pelvic girdle to the shell has resulted in shifts in the origin of most hip muscles onto the interior of the shell. To test how variation in muscle arrangement might influence muscle function during different locomotor behaviors, we combined measurements of muscle leverage in five major hindlimb muscles with data on muscle use and hindlimb kinematics during swimming and walking in representative semiaquatic cryptodires and pleurodires. We found substantial differences in muscle leverage between the two species. Additionally, we found that there were extensive differences in muscle use in both species, especially while walking, with some pleurodire muscles exhibiting novel functions associated with their derived musculoskeletal lever system. However, the two species shared similar overall kinematic profiles within each environment. Our results suggest that changes in limb lever systems may relate to changes in limb muscle motor patterns and kinematics, but that other factors must also contribute to differences in muscle activity and limb kinematics between these taxa.