<p>Horses (<i>Equus caballus</i>) and donkeys (<i>E. asinus</i>) are closely related species with different evolutionary histories: their ancestral forms have different social systems related to their adaptations to different ecosystems, exhibiting female defense and resource defense polygyny respectively. We explored any plasticity of response and possible effects of phylogeny and habitat on these species in a feral state, comparing phylogenetic and habitat effects on behavior. We examined two feral horse populations in similar habitat in western Utah, USA, and two feral donkey populations in different habitat types (central Utah Colorado Plateau and central Arizona Sonoran Desert, USA), over 4 years. Species differences were observed: all donkeys spent more time feeding, moving, and lying down than horses, with horses standing more. Donkeys in the Sonoran Desert spent more time feeding and moving, and less time standing and lying down than on the Colorado Plateau. Horses showed less agonistic and affiliative behavior than donkeys. Between species there was no difference in network degree between horses and donkeys, and donkeys had a more saturated network with higher eigenvector centrality but lower clustering coefficient and fewer connected components than horses. Within a species, we found differences between horse populations in network degree, components, and edge density but no difference between donkey populations. Flexibility in how behavior is expressed reflects an interaction between a species’ habitat and their behavioral response to that habitat. Moreover, phylogenetic history seemingly plays a strong role in the behavioral ecology of a species, even after they are domesticated and become feralized.</p>