Objectives Internal bone structure, both cortical and trabecular bone, remodels in response to loading and may provide important information regarding behavior. The foot is well suited to analysis of internal bone structure because it experiences the initial substrate reaction forces, due to its proximity to the substrate. Moreover, as humans and apes differ in loading of the foot, this region is relevant to questions concerning arboreal locomotion and bipedality in the hominoid fossil record. Materials and methods We apply a whole‐bone/epiphysis approach to analyze trabecular and cortical bone in the distal tibia and talus of Pan troglodytes and Homo sapiens. We quantify bone volume fraction (BV/TV), degree of anisotropy (DA), trabecular thickness (Tb.Th), bone surface to volume ratio (BS/BV), and cortical thickness and investigate the distribution of BV/TV and cortical thickness throughout the bone/epiphysis. Results We find that Pan has a greater BV/TV, a lower BS/BV and thicker cortices than Homo in both the talus and distal tibia. The trabecular structure of the talus is more divergent than the tibia, having thicker, less uniformly aligned trabeculae in Pan compared to Homo. Differences in dorsiflexion at the talocrural joint and in degree of mobility at the talonavicular joint are reflected in the distribution of cortical and trabecular bone. Discussion Overall, quantified trabecular parameters represent overall differences in bone strength between the two species, however, DA may be directly related to joint loading. Cortical and trabecular bone distributions correlate with habitual joint positions adopted by each species, and thus have potential for interpreting joint position in fossil hominoids.