We advance on the knowledge of Eigenmanniinae by proposing a hypothesis of phylogenetic relationships based on the parsimony analysis of a diverse set of 144 anatomical characters, 12% of them treated as quantitative and 88% treated as qualitative (8% external morphology, 51% osteology, 21% myology, and 8% neuroanatomy). Thirty‐seven of 45 valid species of Eigenmanniinae are examined in the study, including the incertae sedis species “Eigenmannia” goajira. The final tree yields new insights on species relationships, thus, producing a new classification to Eigenmanninae. Our analysis recovered the monophyly of Eigenmanniinae, Archolaemus, Eigenmannia, and Rhabdolichops. Eigenmannia is proposed as monophyletic based on four morphological synapomorphies, one of which exclusive to the genus. Japigny is proposed to be the sister group of all remaining Eigenmanniinae and “E.” goajira to be the sister group of Archolaemus. The hypothesis of monophyly of Distocyclus including D. conirostris and D. guchereauae is rejected. Consequently, D. guchereauae is included in Eigenmannia, and a new genus is established to include “E.” goajira. A taxonomic key to all genera is provided. In addition, this study highlights the critical role played by a diverse set of anatomical and quantitative characters without discretization on phylogenetic reconstructions.