Polycera alabe and Polycera atra are closely related opisthobranch sea slugs found in coastal habitats along the eastern Pacific. Both species are extremely variable in external coloration and some of this variation appears to be correlated with geographic range. To determine the phylogenetic relationships and genetic structure of P. alabe and P. atra molecular phylogenies were generated using two genes: H3 (nuclear) and 16S (mitochondrial). Sequence data indicate that populations of P. atra are genetically homogeneous and lack geographic structure along the range of the species. In contrast, Polycera alabe consists of three previously unrecognized, distinct clades with overlapping ranges. The northernmost clade of P. alabe is sister to P. atra, thus the current definition of P. alabe constitutes a paraphyletic assemblage. The southernmost clade presents morphological differences in the radula compared to the other two clades. These data suggest that P. alabe is most likely a species complex.