Similar phenotypic traits can evolve independently in closely related lineages when these lineages are exposed to similar selective pressures (i.e. parallel evolution), while unique histories (i.e. historical contingencies) can also shape phenotypic variation. Here, we addressed the importance of parallel evolution and historical contingency on the morphological variation in sympatric morphs (deep-body and elongate-body) of the genus Astyanax from two different systems (Lake Catemaco and Río San Juan) based on analysis of trophic ecomorphology and geometric morphometrics of body shape. Parallel evolution due to adaptive divergence associated with morphs better explained the variation in trophic ecomorphology, while body shape variation was better explained by historical contingencies. Related to trophic ecomorphology evolution, the elongate-body morph from both systems showed a longer snout, longer ascending process of premaxilla, fewer cuspids on the anterior tooth of premaxilla and acute premaxillary angles associated with parallel evolution (with opposite patterns in the deep-body morph). A higher degree of similarity in body shape between sympatric morphs than between morphs from allopatric systems accounted for the morphological evolution related to historical contingencies. This study highlights how parallel evolution and historical contingency differentially influenced several aspects of phenotype (trophic morphology and body shape, respectively) in the morphological evolution of the genus Astyanax.