Although habitat attributes of black-tailed prairie dog (Cynomys ludovicianus) colonies have been described for central and northern portions of the species' geographic range, little is known about these associations at the southern edge of this species' distribution. Because high-quality habitats are expected to be scarcer at the edge of the species' geographic range, different patterns of habitat selection might emerge in these populations. We analyzed habitat selection by black-tailed prairie dogs in a human-disturbed mosaic of desert grasslands and shrublands in northwestern Chihuahua, Mexico. We contrasted 151 used and 133 unused habitat units producing 11 case-control logistic regression models to explain site occupancy by prairie dogs with different combinations of environmental variables. Prairie dogs from Chihuahua occupy sites similar in most respects to sites in more northern regions, although these prairie dogs appear to be more tolerant of increased shrub density and reduced herbage cover. We found that site occupancy was best modeled by positive effects of soil moisture level, cover of forbs, cover of unpalatable vegetation, cover of bare ground, and amount of prairie-dog colony area within 1 km and by the inverse of altitude, shrub density, herbage height, and amount of hostile habitat within 1 km. The 2 most significant variables were herbage height and shrub density, which might reflect the prominent role that visibility plays in habitat selection by prairie dogs. In contrast, we found weak evidence that human features have significant impacts on site occupancy by prairie dogs. Our results support the prediction that environmental conditions of sites used by prairie dogs in edge regions partially differ from those observed in more northern latitudes. We suggest that reserve managers focus conservation efforts on areas with short vegetation, low density of shrubs, and high herbage cover, conditions that could be promoted by controlled burns, herbage mowing, and mechanical removal of shrubs.