The unified species concept and a criterion of limited homogenizing gene flow as evidenced by genetic and morphological markers were applied to species delimitation within Navarretia sinistra. Concordant patterns of variation diagnose two morphologically cryptic species. As a consequence, the basionym Gilia linearifolia is here lectotypified and re-established for this long neglected epithet. Navarretia linearifolia shows strong differentiation from N. sinistra in allozyme data and DNA sequences from chloroplast regions, nrDNA, and introns of the low copy nuclear genes idhA, idhB, and g3pdh. In macroscopic features, N. linearifolia differs from N. sinistra primarily in tendencies, rather than absolute differences. Two finer-scale features are diagnostic: pollen sexine sculpturing and mature seed color. The combination Navarretia linearifolia subsp. pinnatisecta is made for the large flowered populations of this species geographically restricted to the NW region of the California floristic province. The smaller flowered N. linearifolia subsp. linearifolia extends from California to Washington, with a more westwardly distribution compared to N. sinistra, which ranges east into Idaho, Utah, and Colorado.