We examined the phylogenetic relationships among populations of the Mexican endemic and endangered Phillips' kangaroo rat, Dipodomys phillipsii (Rodentia: Heteromyidae), using mitochondrial (cytochrome-b and 12S ribosomal RNA) and nuclear (growth hormone receptor and interphotoreceptor retinoid-binding protein) genes for a total of 3,110 base pairs. Gene sequences were analyzed under maximum-likelihood and Bayesian models of phylogenetic inference. Analyses of the mitochondrial genes converged on essentially identical gene trees in which D. phillipsii is divided into 2 well-supported clades. The Mexican Plateau clade of D. phillipsii, formerly recognized as D. p. ornatus, is herein returned to full species status as D. ornatus. The southern clade of D. phillipsii retains the subspecies D. p. oaxacae, D. p. perotensis, and D. p. phillipsii. D. ornatus, D. phillipsii, D. elator, and D. merriami form a well-supported, but unresolved polytomy. Analyses of the nuclear genes show the same fundamental subdivision within D. phillipsii but do not provide additional resolution within the 4-species polytomy. Based on analyses of divergence times, we place the separation of these 4 species near the middle Pliocene, which suggests that the morphotectonic processes that gave rise to the Trans-Mexico Volcanic Belt may have influenced diversification in Mexican species of Dipodomys. Synonymies of D. phillipsii and D. ornatus are provided along with a key to the subspecies of D. phillipsi and D. ornatus.