Once encompassing as many as 9 species of pocket gophers spread across most of the Mexican Altiplano, the genus Pappogeomys is now restricted to a single species, P. bulleri, occupying the mountains, tablelands, and coastal plains near the western end of the Trans-Mexican Volcanic Belt in west-central Mexico. Herein, we review the taxonomic history of Pappogeomys and examine relationships among populations of P. bulleri from throughout the geographic range of the species based on analyses of nonpreferentially stained karyotypes and mitochondrial and nuclear sequence data. Results of these analyses are concordant and reveal 3 major clades of P. bulleri that are separated by major physiographic features of the region, including the Sierra Madre del Sur and drainages of the Río Grande de Santiago, Río Ameca, Río Ayuquila, and Río Armería. We reduce the number of subspecies of P. bulleri from 9 to 5 valid forms and provide a revised synonymy of the species.