We examined the genetic population structure for the Great Plains Toad (Bufo cognatus) in the Chihuahuan Desert of southern New Mexico in order to discern at what spatial scale genetic differentiation is apparent. In addition, we tested whether habitats in the Chihuahuan Desert of southern New Mexico differed in their resistance to gene flow in B. cognatus. We used microsatellites to estimate genetic differentiation in populations that varied in distance from 1 to 60 km. Of 120 pairwise tests of genetic differentiation, 44 were significant. However, differentiation was low between all sites (FST = 0.0–0.087), almost all of the genetic variation being within populations (96.3%). Compared to published studies of other anuran species, populations of B. cognatus in southern New Mexico are among the most genetically homogenous anuran species. Significant isolation by distance did occur over all populations despite the genetic similarity, suggesting that differentiation does occur at a broader scale. In addition, several landscape-based models of gene flow were produced and tested against the allelic data. A community model assigned each plant community a different level of resistance to gene flow. This model was not found to describe the estimated genetic variation between populations better than simple Euclidean distance. However, the river model, which assigned low resistance to the aquatic habitats including the Rio Grande, described the estimated genetic variation better than Euclidean distance, suggesting that the Rio Grande, and potentially other rivers throughout the toad's range, may act as a route of dispersal for B. cognatus, reducing genetic differentiation among distant populations.