Ghost electric knifefishes (Gymnotiformes: Apteronotidae) are a dominant component of the species diversity and biomass of large lowland rivers in Greater Amazonia, including 77 species that exhibit diverse craniofacial morphologies associated with trophic and secondary sexual traits. Here we use open-source computed micro-tomography (µCT) scans to generate 3D reconstructions for a majority of apteronotid species and almost all valid genera, and geometric morphometric and phylogenetic analyses to explore patterns of skull evolution. As with most vertebrates, principal component 1 (PC1) summarizes variance from brachycephalic to dolichocephalic morphologies, previously described as heterocephaly, and PC2 summarizes variance from recurved (upturned) to decurved (downturned) snout morphologies, described here as heterorhynchy. Phylomorphospace and traitogram analyses found instances of both convergent and divergent evolution along both of the first two PC axes, as well as a preponderance of clades characterized by morphological stasis or phylogenetic conservatism. Certain phenotypic combinations predominate among species and clades, including elongated-downturned snouts and foreshortened-upturned snouts, while other phenotypic combinations are not observed, including elongated-upturned snouts and foreshortened-downturned snouts. These results highlight the power of 3D geometric morphometrics in the study of craniofacial evolution and indicate developmental or functional constraints in the evolution of craniofacial phenotypes in an ecologically dominant clade of riverine Amazonian fishes.