Aplodontia rufa (mountain beaver) is considered the sole remaining extant genus and species of an ancient lineage that once broadly inhabited the Great Basin and is now restricted to the Pacific Northwest and portions of California and Nevada. Aplodontia rufa californica in Nevada is distributed patchily at the edge of mountain beaver distribution. Due to concern over the status of these populations this subspecies is listed in Nevada as sensitive. The Nevada Department of Wildlife is concerned about the status of Aplodontia rufa californica populations scattered across areas of central western Nevada and has worked to gain an understanding of the subspecies' current distribution and numbers. Because there is a lack of a thorough genetic analysis of these populations in Nevada, this study aims to assess the evolutionary relationships and connectivity of populations within Nevada and California. Therefore, we sampled each of the 9 known localities of Aplodontia rufa in Nevada, as well as 4 sites from the type locality region of the central Sierra Nevada Mountains of California for comparison, using mitochondrial DNA for phylogenetic and network analyses. Additionally, we used microsatellite markers to assess connectivity of populations within Nevada and to proximate California populations. We found that Nevada populations share mitochondrial DNA haplotypes with California populations and therefore belong to the same subspecies. Furthermore, we found evidence of gene flow between Nevada and California populations. Within Nevada, we detected population differentiation that suggested fragmented populations with restricted connectivity. The results of this study will allow Nevada wildlife managers to develop targeted management strategies to enhance connectivity between populations where it is lacking, to protect connectivity that exists, and also to conserve habitat required by this species. This study increases our understanding of this unique and ancient rodent species at the edge of its distribution.