The phylogenetics of eight species of the Peromyscus truei and P. boylii species groups from 15 populations were analyzed based on mitochondrial DNA sequence differentiation, using 13 hexanucleotide specific restriction enzymes. P. difficilis, P. nasutus, and P. attwateri were found to be members of the same clade. P. leucopus was not found to be closely related to any of the species of the boylii or truei species groups. Phylogenetic interpretations for the remaining species differed based on Wagner and Dollo parsimony analyses. P. true appears to be most closely related to P. gratus based on Wagner parsimony and the phenetic analysis, while the relationship of P. gratus to other species could not be resolved based on Dollo parsimony.