The systematics and phylogeography of the San Diego pocket mouse (Chaetodipus fallax), a species restricted to the Baja California Peninsula and adjacent southwestern California, were assessed using sequences of the mitochondrial cytochrome-b gene (Cytb). Genetic relationships were evaluated among the 6 recognized subspecies of C. fallax (including the island population, C. f. anthonyi) in 3 geographic regions from individuals representing 22 populations. Analysis of molecular variance and multiple phylogenetic analyses indicated 3 main clades: northern populations in the southwestern Mojave Desert and Los Angeles Basin north of the Salton Trough; central populations from south of the Salton Trough and throughout the state of Baja California; and southern populations from west of the Vizcaíno Desert in Baja California Sur and adjacent Isla Cedros. These clades do not correspond to the currently recognized subspecies, and each could be considered a distinct subspecies pending analysis of nuclear DNA or characters (e.g., morphology) encoded by nuclear DNA.