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The southern pocket gopher, Thomomys umbrinus, currently contains 17 subspecies distributed from southeastern Arizona and southwestern New Mexico southward into the Trans-Mexico Volcanic Belt (TMVB) of central Mexico. Here we reevaluate relationships within this species, which, based on previous studies, is composed of 3 genetically divergent clades. Multilocus phylogenetic analyses uphold these clades (Northern Desert, Central Plateau, and TMVB) as well as the monophyly of T. umbrinus with respect to the 3 other species in the T. umbrinus complex (T. atrovarius, T. nayarensis, and T. sheldoni). Reanalysis of published allozyme data shows a pattern of isolation by distance consistent with the hypothesis of gene flow among the 3 T. umbrinus clades. Species tree analyses of these clades reveal 4 divergent lineages (2 within the TMVB clade), which we recognize herein at the subspecies level. Cranial morphometrics show a moderate level of morphological separation among these clades in multivariate space. The present center of diversity of the T. umbrinus species group is in the southern Sierra Madre Occidental, which also appears to be the center of origin of the T. umbrinus complex. A synonymy of T. umbrinus is provided.