The Navajini, a clade of Neotropical electric fishes within the family Apteronotidae, exhibit exceptional craniofacial diversity that reflects a dynamic interplay of evolutionary forces. This study examines the morphological, ecological, and developmental drivers of phenotypic diversification in this group, which includes some of the most specialized skull morphologies among South American freshwater fishes. We integrate 3D geometric morphometrics, high-resolution micro-computed tomography (micro-CT), and multivariate statistical analyses within a robust phylogenetic comparative framework to assess patterns of skull shape evolution across the clade. Ancestral state reconstruction and tests for phylogenetic signal reveal that key cranial traits such as lower jaw elongation, opercle morphology, and maxilla orientation are not randomly distributed but instead show significant phylogenetic structure and ecological relevance. Morphological disparity is strongly influenced by sexual dimorphism in certain lineages, particularly those exhibiting hypertrophied male traits, while other groups display more conservative, modular cranial architectures. We find that access to novel regions of morphospace has been facilitated by shifts in feeding ecology and developmental modularity, enabling trophic specialization and repeated convergent evolution among ecologically similar taxa. These findings support a model in which cranial evolution is shaped by both adaptive responses to ecological opportunity and intrinsic developmental constraints. Overall, this work sheds light on the mechanisms generating phenotypic diversity in Apteronotidae and contributes to a broader understanding of how ecological and evolutionary processes interact to shape morphological evolution in Neotropical freshwater fishes.