Edaphic-endemic plant taxa are often interpreted as recently derived entities that evolved in situ, with genetic divergence driven by substrate specialization. However, little is known about the evolution of specific edaphic-endemic taxa, particularly the role that soil conditions may play in their initial divergence and continued persistence. Our study focuses on Ceanothus roderickii, a strict specialist on soils derived from a single outcrop of the geological material gabbro located in south-western El Dorado County, California. In order to elucidate the evolutionary history of C. roderickii we sequenced the third intron of the low-copy nuclear gene nitrate reductase (NIA) for individuals representing four populations of C. roderickii and a wide taxonomic and geographic sampling of closely related plants, including 37 populations of Ceanothus cuneatus and a single representative from 16 other taxa. Analysis of NIA shows that C. roderickii is closely related to C. cuneatus var. cuneatus, a widely distributed taxon found on a diversity of soils. Ceanothus cuneatus var. cuneatus is paraphyletic and comprises two major geographic groups, one coastal and one interior, the latter containing C. roderickii. Thirteen soil chemistry variables were assayed in 42 populations of C. cuneatus representing the wide geographic range of this species, and in 10 populations of C. roderickii. Analysis of these data indicates that evolution of C. roderickii was associated with specialization to nutrient-deficient forms of gabbro-derived soil. Soil chemistry associations of C. cuneatus var. cuneatus and C. roderickii are most divergent where the species come into close contact on gabbro, with C. cuneatus var. cuneatus occupying comparatively nutrient-rich forms of gabbro-derived soils, a result that is consistent with reinforcement.