The surfperch genus Embiotoca currently comprises two species, Embiotoca jacksoni, the black surfperch, and Embiotoca lateralis, the striped surfperch. Originally, however, Louis Agassiz described a third species in the genus Embiotoca, the rainbow surfperch, Embiotoca caryi. This latter name was changed by Louis’ son, Alexander, to Hypsurus caryi, a name that remains valid. In this study, new molecular data (3545 bp of DNA from four mitochondrial and two nuclear DNA regions) indicated that the rainbow surfperch should be retained within the genus Embiotoca, a result consistent with recent morphological data. Adaptive radiation combined with sexual selection resulting in rapid morphological changes in the rainbow surfperch may have contributed to the conflicting position of this species.