The California Floristic Province (CA-FP) is the most species-rich region of North American north of Mexico. Several hypotheses have been proposed to explain why this region is exceptionally diverse, including that it harbors many recently diverged clades with weak or no barriers to reproduction.

Salvia subgenus Audibertia is a conspicuous element of the CA-FP, with multiple species often occurring in sympatry. Using 305 nuclear loci and both organellar genomes, we reconstruct species trees, examine genomic discordance, conduct divergence-time estimation, and analyze contemporaneous patterns of geneflow and mechanical reproductive isolation.

Despite strong genomic discordance, an underlying bifurcating tree is supported. Organellar genomes capture additional introgression events not detected in the nuclear genome. Most interfertility is found within clades and species are generally not mechanically isolated.

Rapid, recent speciation with some horizontal geneflow during the rise of Mediterranean climate is the underlying cause of extant diversity in subgenus Audibertia. Geneflow has largely not facilitated speciation. Its signal in the nuclear genome seems to mostly be erased by backcrossing, but organellar genomes each capture different events of historical geneflow, perhaps characteristic of many lineages in the CA-FP. Mechanical reproductive isolation is likely only part of a mosaic of factors limiting geneflow.