Diverse geological and environmental pressures can impact morphological evolution. Yet, it remains unclear how ecological factors affect similar species sharing a trophic niche. Here, we investigate populations of Bramocharax and Astyanax fishes, two morphs inhabiting lakes in Mexico and Central America. Using geometric morphometric analyses of micro-CT scanned skulls, we found both groups exhibit craniofacial variation along a latitudinal cline of four lake populations. This ecomorphological divergence evolved between both morphs despite their sympatry. Southern Nicaraguan populations demonstrate tooth and cranial differences between the morphs while two northern Mexican populations exhibit similarity in dentition and cranial shape. Southern lake populations are geologically much older, possibly enabling evolution and elaboration of more diverse feeding niches. This resulted in southern Bramocharax populations displaying more streamlined cranial structure with longer, more numerous unicuspid maxillary teeth compared to Astyanax. Further, northern Mexican populations inhabit geologically younger lakes, showing more similarity in morphology. We propose this may be due to a shorter divergence time compared to the Nicaraguan lakes. Patterns of morphological evolution across all four lakes, however, suggest Bramocharax fish evolve similar physiological traits to Astyanax via parallel evolution. This work provides an important case study for differential effects of geological and ecological pressures on morphological divergence in closely-related animals.