The family Aplodontiidae contains a single, monotypic extant genus, Aplodontia (mountain beaver), which was 1st described by Rafinesque in 1817. Phylogenetic studies have shown that it is the sister lineage to squirrels. Aplodontia rufa is endemic to the Pacific Northwest and ranges from central California to British Columbia. Currently, 7 described subspecies are recognized based on morphological taxonomic studies. In this study, mitochondrial and nuclear genes were sequenced to infer molecular phylogenies of A. rufa. One of the goals of this study was to test the current taxonomic hypothesis based on morphology with molecular data. Another goal was to incorporate geographic information to elucidate distributions of major clades. Our results support the previously held subspecies designations based on morphological taxonomy, with 1 main exception: we determined that within A. rufa, the subspecies A. rufa rainieri and A. rufa rufa north of the Columbia River represent a single lineage and should revert to the name A. rufa olympica. Although we revised geographic boundaries for some groups (A. r. rufa, A. r. olympica, A. r. pacifica), only the conservation status and management of A. r. olympica (previously 2 subspecies) in Canada may be affected. Our findings support the continued conservation efforts for the isolated and endangered lineages present in coastal California.