Phylogeographic relationships among 26 populations from throughout the geographic range of the Peromyscus eremicus species group are described based on sequence data for a 699-bp fragment of the mitochondrial DNA COIII gene. Distance, maximum-likelihood, and maximum-parsimony analyses of phylogenetic trees generated under four separate character-weighting strategies and representing five alternative biogeographic hypotheses revealed the existence of a cryptic species (Peromyscus fraterculus, previously included under P. eremicus) on the Baja California Peninsula and adjacent southwestern California and two distinct forms of P. eremicus, one from the Mojave, Sonoran, and northwestern Chihuahuan regional deserts (West) and one from the remainder of the Chihuahuan Desert (East). Distinctiveness of P. fraterculus is supported by previous morphometric and allozyme analyses, including comparisons with neighboring P. eremicus and parapatric P. eva, with which P. fraterculus shares a sister taxon relationship. Divergence of the eva + fraterculus, West + East eremicus, and P. merriami haplotype lineages likely occurred in the late Neogene (3 Ma), in response to northern extension of the Sea of Cortéz and elevation of the Sierra Madre Occidental; divergence of eva from fraterculus is concordant with the existence of a trans-Peninsular seaway during the Pleistocene (1 Ma); and divergence of West from East eremicus occurred during the Pleistocene pluvial-interpluvial cycles, but well before the Wisconsinan glacial interval. The sequence of divergence within the eremicus species group and causal association of geological events of the Neogene and Holocene provide a working hypothesis against which phylogeographic patterns among other arid-adapted species of the warm regional deserts of North America may be compared.