AbstractThe complex geological history and tropical climate of Mesoamerica create a rich source of biodiversity from which we can study evolutionary processes. Here, we discuss highly divergent forms of lake-dwelling fishes distributed across southern Mexico and Central America, originally recognized as members of different genera (AstyanaxandBramocharax). Recent phylogenetic studies suggest these morphotypes group within the same genus and readily hybridize. Despite genetic similarities,Bramocharaxmorphs exhibit stark differences in cranial shape and dentition. We investigated the evolution of several cranial traits that vary across morphs collected from four lakes in Mexico and Nicaragua and discovered an ecomorphological cline from the northern to southern lakes. Northern populations of sympatric morphs exhibit similar cranial shape and tooth morphology. Southern populations ofBramocharax, however, have more maxillary teeth, larger unicuspid teeth, an elongated snout and a streamlined cranium compared toAstyanax. The divergence of craniofacial morphology in southern lakes likely evolved in response to environmental pressures. We discuss the ecological differences across the four lake systems in terms of geological history and trophic dynamics. In summary, our study suggests thatBramocharaxare likely locally-adapted members derived fromAstyanaxlineages, highlighting the complex evolutionary history of theAstyanaxgenus.