We investigated intraspecific variability in phenotype and population genetic structure of yellowhead jawfish Opistognathus aurifrons from 4 different locations in the Caribbean region: South Florida (USA), Bimini (Bahamas), St. Thomas (US Virgin Islands), and Aruba. Discriminant function analysis (DFA) of 9 melanistic traits in the head region resulted in clear separation between Bimini and the other 3 populations. South Florida, St. Thomas, and Aruba slightly overlapped in patterning, with St. Thomas forming the transition between South Florida and Aruba. DFA of 17 morphometric characters elucidated differentiation among the 4 populations with some overlap between populations. Analysis of concatenated cytochrome c oxidase subunit I (COI) and mitochondrial control region (mtCR) sequences revealed substantial differences among O. aurifrons populations (pairwise Φ ST = 0.185−0.566), although there was a lack of reciprocal monophyly. Differences in patterning and morphometrics constituted different phenotypes that predominated in each location, with high levels of genetic differentiation between sampled populations. Bimini was most divergent in phenotype, while Aruba was most divergent in genetics. As such, variations in phenotype and genetics are not congruent for O. aurifrons investigated in this study.