The degree of concordance between patterns of divergence in genetic and morphological characters provides insight into the process of evolutionary diversification. We analyzed species-wide morphological variation in a broadly distributed species of small mammal, the bushy-tailed woodrat (Neotoma cinerea), for comparison against a recently developed mitochondrial phylogeny. We focused our analyses on patterns of qualitative and quantitative craniodental morphological variation throughout the distribution of this taxon. We found strong concordance between the morphology of one prominent craniodental feature (sphenopalatine vacuity) and the major mitochondrial lineages, but only minimal differentiation in overall morphometric variation between these clades. Further, in contrast to the largely east–west subdivision of mitochondrial and sphenopalatine vacuity variation, cluster analyses of morphometric variation revealed a north–south morphological subdivision irrespective of mitochondrial clade. Our combined character sets are best explained by a deep history of evolutionary divergence within this taxon accompanied or followed by broad-scale convergent or parallel evolution.