Phylogenetic relationships of the Mexican endemic and endangered Nelson's woodrat, Neotoma nelsoni (Rodentia: Cricetidae), were examined using three mitochondrial genes (cytochrome-b, 12S ribosomal RNA, and 16S ribosomal RNA) for a total of 2,140 base pairs. Gene-sequences were analyzed using maximum likelihood and Bayesian models of phylogenetic inference. Independent analyses of the three gene-sequences converged on essentially identical gene trees, all showing N. nelsoni to be a sister lineage to N. leucodon from Durango, Mexico. Given the relatively low level of divergence of sequence of cytochrome-b between N. nelsoni and N. leucodon (3.3% using the Kimura two-parameter model, which is less than variation within N. leucodon) and the current absence of reliable diagnostic morphological characters to distinguish N. nelsoni from N. leucodon, N. nelsoni is recognized as a subspecies of N. leucodon. Based on molecular estimates of times of divergence, phyletic diversification in the species-group N. micropus (which includes N. leucodon nelsoni) began near the Middle Pleistocene and N. leucodon nelsoni diverged from other Mexican populations of N. leucodon during the Late Pleistocene. The repeated Pleistocenic cycles together with the final periods of volcanic activity in the eastern part of the Trans-Mexico Volcanic Belt may have played a major role in early differentiation in this lineage.