Previous studies have postulated that the Streptanthus glandulosus Hook. complex (Brassicaceae) originated through gradual range contraction and isolation of populations of an ancestral species distributed in California, United States. Here, we integrate patterns of interfertility, morphology, ITS, and chloroplast DNA (cpDNA) variation to generate a classification system reflective of the phylogeny of this group. As a result, we propose a single species, S. glandulosus, with 10 subspecies, to constitute the complex. Populations of S. glandulosus subsp. glandulosus distributed north of the San Francisco Bay are now divided between two new subspecies, S. glandulosus subsp. arkii M. S. Mayer and subsp. raichei M. S. Mayer, diagnosable through molecular apomorphies, perianth color, and fruit orientation. The name S. peramoenus Greene is synonymized to S. glandulosus subsp. glandulosus and is further lectotypified.