Thomomys atrovarius is redescribed to include the smooth-toothed pocket gophers that inhabit dry, thornscrub vegetation along the Pacific versant of the Sierra Madre Occidental of Mexico from northern Sinaloa into western Durango, northwestern Jalisco, and western Nayarit. Molecular analyses of mitochondrial and nuclear DNA sequences (including historical samples from museum skins) show high levels of genetic differentiation between T. atrovarius and T. umbrinus of the Sierra Madre Occidental (15.4% cytochrome-b divergence) and Mexican Central Plateau (16.9% divergence). Roughly coincident morphometric and genetic gaps divide T. atrovarius into 2 subspecies, T. a. parviceps in the north and T. a. atrovarius in the south, with probable intergradation in between. Most specimens of T. atrovarius, especially those of the southern subspecies, are distinguished easily from specimens of T. bottae and T. umbrinus on the basis of fur texture, and an analysis of cranial morphometrics shows little overlap between T. atrovarius and other Thomomys clades in Mexico. An analysis of niche parameters shows significantly different climate envelopes for T. atrovarius compared with other species of Thomomys, and a biogeographical review suggests that T. atrovarius has ancestral affinities to the south of its current distribution. A synonymy of T. atrovarius and a key to the currently recognized species of Thomomys in mainland Mexico are provided.