Most populations of Salvia pachyphylla occur along mountain ranges adjacent to the Mojave Desert of southern California, southwestern Nevada, and northern Baja California, Mexico. A smaller disjunct group occurs in eastern Arizona near the southern edge of Navajo and Hopi reservation lands near Winslow, AZ. This study was undertaken to determine whether there are morphologically and genetically distinct geographical groups within S. pachyphylla and whether these groups form a cohesive unit easily separated from S. dorrii. Specimens of S. pachyphylla and broadly sympatric taxa in S. dorrii were examined in a morphometric analysis of twelve characters. A preliminary molecular analysis using the nuclear ribosomal DNA internal transcribed spacers (ITS-1 and ITS-2) and the embedded 5.8 S subunit was also performed on the same taxa. Morphometric analysis supports the continued recognition of S. pachyphylla and S. dorrii as distinct species and the recognition of three subspecies within S. pachyphylla, requiring two new subspecies, eremopictus and meridionalis, described here. The molecular data support the recognition of the S. dorrii species complex as a whole, but do not support the separation of S. dorrii and S. pachyphylla as distinct species, although the Mexican populations of S. pachyphylla appear genetically distinct.