Taxonomic affinity of Peromyscus boylii sacarensis was examined using DNA sequences from the mitochondrial cytochrome-b gene. Maximum parsimony and genetic distance analyses were used to examine the phylogenetic relationship of this taxon to other closely related members of the P. boylii species group (P. beatae, P. boylii rowleyi, P. levipes ambiguus, P. l. levipes, and P. simulus). All analyses, despite differential weighting of transitions and nucleotide positions (1st, 2nd, and 3rd) or method of calculating genetic distances, resulted in similar topologies with P. b. sacarensis forming the sister group to P. beatae. Our data suggest that P. b. sacarensis should be aligned taxonomically with P. beatae instead of its current placement in P. boylii and that 3 genetic subunits exist within P. beatae.