Pappogeomys alcorni is a peripherally isolated species that currently is designated as a rare species in Mexico. There are only 4 known museum specimens, all collected between the years 1950 and 1966, and recent attempts have failed to locate individuals in the wild. Although only 1 new specimen (skin only) has been collected since the original systematic work on P. alcorni, new analytical methods permit reexamination of existing specimens. DNA was isolated from a 48-year-old museum skin to investigate the phylogenetic relationship of this rare taxon to other species of Pappogeomys and Cratogeomys. Phylogenetic analysis based on 424 base pairs of the mitochondrial cytochrome-b gene and morphometric analysis of 101 individuals of Pappogeomys indicate that P. alcorni is a geographically disjunct subspecies of P. bulleri rather than a monotypic species.