Limb bone morphology often correlates with functional demands placed on animals by the environment. Comparisons of limb bone allometry in functionally divergent turtle taxa indicate highly specialized lineages show extensive flattening of the humerus. In Sea Turtles this contributes to flipper-shaped forelimb morphology that facilitates lift-based swimming (i.e., underwater flight). In contrast robust humeri and femora in terrestrial tortoises may reflect specializations for resisting high torsional loads during terrestrial walking and digging. However, it is unknown whether allometric patterns of ecomorphological divergence can be detected among more closely related lineages within clades that encompass species with diverse ecological habits. To test whether limb bone size and shape vary among closely related taxa that live in divergent habitats, we used phylogenetic comparative methods to assess scaling patterns and overall morphology of the humerus and femur of 27 emydid turtle species representing four genera: Graptemys (semiaquatic), Pseudemys (semiaquatic), Trachemys (semiaquatic), and Terrapene (terrestrial). In general, we found that limb bones of emydid taxa scale isometrically for most length–diameter and length–mass relationships. However, terrestrial Terrapene (box turtles) species exhibit relatively short femora compared with species from the more aquatic genus Trachemys (sliders). The relatively small limb bones of box turtles may promote limb withdrawal into the shell, but without mechanical costs because of high safety factors of turtle limb bones. The comparatively robust forelimb and hindlimb dimensions of Graptemys (map turtles) relative to other emydid clades may reflect habitat and foraging pressures in this group.