Neotoma fuscipes, the dusky-footed wood rat, is a morphologically diverse taxon with recognized intraspecific subdivisions that are based on both quantitative and qualitative morphology. Although there is substantial morphological variation within this taxon, intergradation among the various forms has been observed by previous workers. A recent survey of mitochondrial DNA revealed a high degree of molecular divergence within the taxon. Here, morphological, mitochondrial sequence, and nuclear microsatellite data are examined in a contact zone between 2 reciprocally monophyletic mitochondrial clades. On the basis of concordance of qualitative cranial, glans penes, and molecular characters, the 2 units appear to be genetically isolated from one another, leading to the elevation of N. macrotis to a species separate from N. fuscipes.