The Mojave Desert is characterized by a unique biodiversity and is an area of particular interest for the development of renewable energy facilities, which could impact habitat quality and population connectivity. To begin understanding current habitat connectivity in a Mojave Desert endemic, we examine population genetic characteristics of the Mohave ground squirrel, Xerospermophilus mohavensis. We use microsatellite and mitochondrial data to examine the spatial distribution of genetic variation and to infer regional demographic history and connectivity across the species' range. We also examine the demographic history of individual populations and assess the degree to which X. mohavensis may be hybridizing with its sister species, Xerospermophilus tereticaudus. We find that populations of X. mohavensis group into three regionally defined genetic clusters with admixture among the groups. Patterns of regional genetic subdivision and inferred patterns of colonization are consistent with what would be expected from the location and timing of the historic lake and river systems of the region. On a more recent timescale, most X. mohavensis populations do not appear to have experienced genetic bottlenecks, as would be expected from known population declines. Finally, we find that hybridization between X. mohavensis and X. tereticaudus is limited, and thus, not a source of introgression into the threatened species. The patterns of diversity and regional connectivity that we describe here for the Mohave ground squirrel are a first step in determining critical conservation areas for endemic Mojave Desert fauna.