The deer mouse species group centers around Peromyscus maniculatus and contains four peripherally distributed species. In order to address phylogenetic, taxonomic, and biogeographic questions concerning the westernmost deer mice, we analyzed mitochondrial sequence variation for 174 specimens from California to Washington and compared these to relevant reference specimens. These analyses confirm the genetic distinction of a clade of physiographically bounded deer mouse populations from Southern and Baja California and the close affinity of this clade to the endangered and island-endemic Peromyscus sejugis. In accordance with the phylogenetic species concept and taxonomic priority, we recommend that all populations currently recognized as Peromyscus maniculatus coolidgei (Baja California) and those of Peromyscus maniculatus gambelii from south of the San Francisco Bay and west of the Sierra Nevada mountains be recognized as Peromyscus gambelii. Despite its low level of mitochondrial sequence divergence compared to P. gambelii, the genetic and morphologic distinctness, insular allopatry, and threatened status all argue for the retention of P. sejugis.