A phylogeny of the Neotoma floridana species group of woodrats was inferred using mitochondrial-DNA (mtDNA) restriction sites identified by 17 type-11 restriction endonucleases. Wagner, Dollo, and generalized parsimony analyses revealed a sharp dichotomy among populations of Neotoma albigula found east and west of the Rio Grande. Additional polymorphism among samples of N. albigula from northern Mexico also was detected. Data from mtDNA suggest paraphyly exists within N. albigula and that at least two cryptic species are present within the taxon. Phylogenetic and phenetic analyses of the mtDNA data reveal a sister-group relationship between Neotoma micropus and N. albigula, whereas N. floridana and Neotoma magister form sister taxa to this group. These results clarify discrepancies reported for this species group based on morphologic, allozymic, and karyotypic data. Additionally, Neotoma phenax, Neotoma cinerea, Neotoma mexicana, and Neotoma stephensi were included to provide an intrageneric perspective on relationships within the N. floridana species group. N. mexicana and N. stephensi formed a clade associated with the N. floridana species-group clade with N. phenax and N. cinerea appearing as sole members of branches basal to the remaining Neotoma.