The largest remaining black-tailed prairie dog Cynomys ludovicianus towns in North America are in Mexico, where they coexist with the kit fox Vulpes macrotis, providing a unique opportunity to study the relationship between these threatened species. We hypothesized that the presence of prairie dogs would positively affect the kit fox population in our study area in north-western Mexico, and that these influences would be manifest in home-range size, density and habitat selection. We estimated fox densities fluctuating from 0.32/km2 to 0.8/km2, and radio-telemetry revealed minimum convex polygon home ranges averaging 11 km2. These values are within the bounds of estimates from study sites elsewhere. Foxes used mesquite scrub less than expected, but grassland more than expected in relation to availability. Other habitats, including prairie dog towns, were used at random. Most (65.1% of 43) fox dens were in grassland, and were enlarged kangaroo rat Dipodomys spp. (34.9%) or prairie dog (34.9%) burrows. That kit foxes seemed to select grasslands rather than prairie dog towns was unexpected, particularly as prairie dogs are known to be a major component of kit fox diet. Foxes may reduce the amount of time they spend in prairie dog towns to avoid coyotes, which can be responsible for significant swift fox mortality. In our study area, coyotes were more active in prairie dog towns than in the grassland, where they were regularly shot. However, grassland used by kit foxes is a short-lived product of prairie dog poisoning, which is quickly invaded by scrub, a habitat favoured by coyotes. We conclude that kit fox conservation initiatives in north-western Mexico should be closely linked to conservation of the prairie dog ecosystem.