In an effort to further resolve relationships within the genus Limnanthes and the family Limnanthaceae a phylogenetic study was conducted using one nuclear (nrITS) and two chloroplast (trnL intron and trnS-trnG intergenic spacer) genes. In addition to surveying all currently accepted taxa within Limnanthaceae, an anomalous population of 4-petalous plants from Half Moon Bay, San Mateo County, California, was also included. Further, a series of crossing experiments were performed between Half Moon Bay plants and two closely related species (Limnanthes bakeri and L. macounii). The results of this study confirm the monophyly of two sections within Limnanthes and also suggest that Limnanthaceae may contain as few as four species of Limnanthes and the monotypic genus Floerkea proserpinacoides. Additionally, the molecular phylogenetic results and crossing experiments do not support taxonomic recognition of the Half Moon Bay population, rather it is part of a highly polymorphic Limnanthes douglasii sensu lato.