The Mohave ground squirrel (Xerospermophilus mohavensis) is endemic to the western Mojave Desert of California and is state-listed as Threatened. This species is of conservation concern because of the potential for large-scale renewable energy development within its range. Recent evidence suggests that this threatened species may at least occasionally hybridize with the closely related round-tailed ground squirrel (Xerospermophilus tereticaudus) where the species come into contact. As a result, there is great interest in the distribution of the Mohave ground squirrel, especially where it may come in contact with the round-tailed ground squirrel. One of the least understood portions of the Mohave ground squirrel distribution is around the Hinkley Valley, west of the city of Barstow, where its eastern range limits come into proximity with the round-tailed ground squirrel. To document what is known of the fine-scale distribution of these congeners in this region, we assemble and review all available trapping survey data from this area and combine the field survey data with genetic analyses of recently collected samples. Our evaluation of trapping records confirms that there are no reliable recent reports of Mohave ground squirrels in the Hinkley Valley itself, which has been developed for agriculture. The species appears to be largely restricted to the relatively undisturbed desert habitat west of Hinkley. In contrast, a number of round-tailed ground squirrel records exist for the Hinkley Valley, some dating back to 1977. Using 13 nuclear microsatellite loci from 55 ground squirrel samples collected across this region, we confirm the presence of genetically pure Mohave and round-tailed ground squirrels. However, 3 individuals collected in the Hinkley Valley that were identified as round-tailed ground squirrels on the basis of external characteristics show evidence of Mohave ground squirrel ancestry. In similar fashion, 3 animals from the desert region west of Hinkley were found to have some round-tailed ground squirrel genetic ancestry in spite of external features typical of Mohave ground squirrels. While round-tailed ground squirrels seem to be the dominant species in Hinkley Valley and Mohave ground squirrels seem dominant in the desert environment to the west, hybridization does appear to occur occasionally. Further, when these species hybridize, at least some hybrids are fertile, and backcrossing appears to occur in both parental directions. It is important to investigate this phenomenon more closely to evaluate possible threats to the genetic integrity of the Mohave ground squirrel.