Although the ornate shrew (Sorex ornatus) is widely distributed throughout California and northern Baja California, genetic analyses have shown that it is phylogeographically structured into 3 genetically differentiated regions (southern, central, and northern) within its distribution. These genetic groups might have been separated for more than a million years. In the northern region, ornate shrews cannot be genetically differentiated from their sister taxon, the wandering shrew (S. vagrans). Therefore it has been suggested that northern ornate shrews might have been misclassified. However, by analyzing skull morphology we show that ornate and wandering shrews, as well as the closely related montane shrew (S. monticolus), are well differentiated. Shrews from the northern region have a morphology similar to ornate shrews and not to wandering or montane shrews. Within the ornate shrews, populations across the range differ in morphology. However, morphological differentiation is not concordant with the deep tripartite pattern of genetic differentiation. Our results imply that skull shape differences among populations could be the result of local adaptation, whereas the long history of isolation might have contributed little to morphological differences between species. In addition, these results suggest that wandering shrews might be derived from the postglacial northward expansion of an ancestral population of northern ornate shrews.