Gaps between distributions of closely related species have been noted in the literature but little empirical research exists to explain these patterns. One hypothesis is poor habitat quality occurs within the gaps and therefore prevents species from inhabiting these areas. Multiple examples of gaps between species distributions can be found among different species of pocket gophers. The objective of this research was to analyze a zone of separation between Geomys bursarius and Cratogeomys castanops in southwest Kansas. Habitat suitability maps were produced using Maxent (3.3.2) for each species throughout the study area. Values of habitat suitability and important habitat variables were compared between locations within the zone of separation and presence localities. The most important variable for predicting habitat suitability for G. bursarius was percent sand, while both percent sand and clay were important for C. castanops. Habitats within the zone of separation were significantly less suitable compared to presence localities. Also, important habitat variables (percent sand and clay) were significantly different at presence localities for both species compared to within the zone of separation. These results suggest the zone of separation between populations of G. bursarius and C. castanops is maintained by a trough of lesser quality habitat.