Pseudopimelodidae comprises 50 species allocated in seven genera widely distributed in the Neotropical region, from northwestern Colombia to northwestern Argentina. In order to assess the phylogenetic relationships of Pseudopimelodidae, we collected sequence data from ultraconserved elements (UCEs) of the genome from 52 terminals of Pseudopimelodidae and 19 related taxa. We used a concatenated matrix to assess the phylogenetic relationships by Bayesian inference (BI) and maximum likelihood (ML) searches. Our results strongly support Pseudopimelodidae as monophyletic, arranged in two major clades herein classified in the subfamilies Pseudopimelodinae, and the newly proposed Batrochoglaninae. Pseudopimelodinae is composed by the genus Cruciglanis Pseudopimelodus and Rhyacoglanis, whereas the new subfamily Batrochoglanidae was divided in two tribes, Lophiosilurini, composed by Cephalosilurus plus Lophiosilurus, and Batrochoglaniini, composed by Batrochoglanis and Microglanis.