The potential impact of paleo-drainage basin morphologies on biogeographic patterns of the Tibetan Plateau and East Himalayas has been attracting increasing attention in recent studies (e.g., [13]–[18]). Although Percocypris is likely an ideal system for testing the biogeographical hypotheses, the evolutionary history and even the classification of this group were not well understood because of the difficulty of collecting relevant specimens. To the best of our knowledge, there have been few, if any, studies using a fish genus with the particular distribution pattern found in Percocypris to investigate biogeographic issues of the Southeastern Tibetan Plateau.