The Owens Valley vole (Microtus californicus vallicola) exists in populations fragmented by natural aridity, land cultivation, highways and canals, and local urbanization. We used genetic analysis of six microsatellite DNA markers to investigate potential fragmentation, genetic drift, and geographic divergence of three populations distributed on the northern, southern, and central portions of the range. Our analyses found that the populations have similar levels of heterozygosity, no significant differences in allelic richness, and significant levels of genetic differentiation. With additional samples from intermediate locations, we would be able to better assess levels of gene flow among these populations. Our current results suggest that these populations do not necessarily require active management intervention.