Lilaeopsis masonii is a California state-listed rare species with a wide range of morphologies observed in the field throughout its range, and in herbaria collections. This extensive variation confounds reliable taxonomic identification, particularly for those specimens intermediate between L. masonii and its sister taxon, L. occidentalis. To investigate the genetic basis of this morphological variation, we examined two portions of the Lilaeopsis genome in seven species. Specifically we sought to determine whether L. masonii is sufficiently distinct from its closely related, widespread congener to continue to warrant specific status. DNA sequence analysis of ITS1, 5.8S, and ITS2 nuclear ribosomal DNA revealed no differences between L. occidentalis and L. masonii California collections, and minimal differences between these samples and L. occidentalis collected from the state of Washington, suggesting strongly that these two species form a single clade. A combination of fragment data from three AFLP primers yielded 274 fragments from 29 samples. Genetic Manhattan distance values calculated from the AFLP matrix within species ranged from a low of 1.4 to a high of 6.6, reflecting minor differences among all samples. UPGMA cluster phenograms support the results of the PCA analysis, illustrating a cluster of L. occidentalis masonii samples distinct from other Lilaeopsis species. Because conservation dollars should protect unique evolutionary entities, we suggest that L. masonii be subsumed under L. occidentalis and therefore no longer receive formal state protection.