In the California Floristic Province (CA-FP) and nearby deserts, 19 species of Salvia (Lamiaceae, Mentheae) form a small radiation but an important component of the chaparral and desert communities. Traditionally, two groups within these Californian Salvia have been recognized (usually treated as sections), but relationships within each, to each other, and to other Salvia are unclear. Phylogenetic relationships of all species, with multiple accessions for most, were obtained using chloroplast DNA (cpDNA) and nuclear ribosomal DNA (nrDNA) markers. Ancestral character state reconstruction of both vegetative and floral features was done on the resulting nrDNA tree. Biogeographical analysis of the groups within the CA-FP and adjacent floristic provinces was done in BioGeoBEARS and species diversification assessed with BAMM. Significant conclusions drawn from the study include: 1) California Salvia should be classified into two monophyletic sections, Audibertia (15 species) and Echinosphace, (four species) in the new subgenus Audibertia; 2) subg. Audibertia and the Neotropical subg. Calosphace are sister clades, most closely related to Asian groups, and are likely Asian in origin; 3) nrDNA provides a fairly resolved tree for subg. Audibertia with all species monophyletic; 4) cpDNA and nrDNA trees are strongly incongruent and provide evidence that hybridization and chloroplast capture have played an important role in the evolution of subg. Audibertia; 5) ancestral character reconstruction of states in habit, possession of spines, calyx lobing, and staminal features highlights a complex (sometimes convergent) evolutionary history of this iconic CA-FP lineage; 6) subg. Audibertia arose in desert areas and more recently diversified into the southwestern California region and adjacent regions with the formation of the Mediterranean-like climate; and 7) this diversification exhibits a slight decrease in speciation and an increase in extinction rates over the group's 11 million year history.