Members of the genus Psilorhynchus are small cypriniform fishes adapted for life in the fast flowing streams of the Ganga–Brahmaputra drainage of India and Eastern Nepal and the Ayeyarwady drainage of Northern Myanmar and adjacent China. The systematic placement of Psilorhynchus within existing cypriniform classification schemes has been controversial since the creation of this genus by McClelland in 1839. Over the last 150 years Psilorhynchus has been assigned to, and removed from, the Cyprinidae, Balitoridae, and Cobitidae at least once and has even been placed in its own family, Psilorhynchidae. In this paper we investigate the gill-arch osteology of two species of Psilorhynchus (P. sucatio and P. balitora) and compare their general features to those of a ‘typical’ member of the Cyprinidae. Additionally, we reassess the most recent testable phylogenetic analyses to include species of Psilorhynchus. We conclude based on evidence from gill-arch osteology that Psilorhynchus is more closely related to non-cyprinid cypriniforms than to members of the Cyprinidae.