Hyphessobrycon is one of the most species rich genera in the family Characidae, with more than 160 species. It is well established that Hyphessobrycon is not monophyletic but has been suggested that natural groups can be identified within the larger Hyphessobrycon species group. In this study, we use ultraconserved elements (UCEs) to a) infer the first phylogenomic hypothesis of trans-Andean Hyphessobrycon that includes nearly complete taxonomic sampling (eight of nine valid species), b) test the monophyly of trans-Andean species of Hyphessobrycon and c) explore the placement of the trans-Andean Hyphessobrycon species within the sub-family Stethaprioninae (Characidae). Furthermore, we explore if alternative set of relationships were supported by the data and explore if there is cryptic diversity within the trans-Andean Hyphessobrycon