A comprehensive phylogeny of species relationships of the Auchenipteridae is reconstructed here with a large-scale taxon sampling based on combined morphological and molecular datasets. The hypothesized phylogeny includes most species of Auchenipteridae (97 of 124 valid species) and multiple members of siluriform families as an outgroup (32 species) to embrace the diversity of forms among related catfishes. As the first large-scale phylogeny of the Auchenipteridae, comparison between taxa included information from both morphology (264 characters) and mitochondrial and nuclear molecular markers (3490 nucleotides) from five genes: coI, 16S, rag2, myh6 and SH3PX3. Trees were generated under two different optimality criteria (Maximum Parsimony and Bayesian Inference). A new classification for the family is presented herein to bring the taxonomy more in line with the new phylogenetic hypothesis. The strict consensus tree corroborates the monophyly of superfamily Doradoidea, family Auchenipteridae and its two subfamilies, Centromochlinae and Auchenipterinae. The new classification scheme proposes nine tribes in Auchenipteridae, based on the monophyly of major groups in both subfamilies. Centromochlus, Glanidium and Tatia are each recovered as paraphyletic. To maintain a monophyletic classification, some species treated as Tatia and Centromochlus are assigned to genera not previously recognized as valid.