The watershed of the Wuyi-Xianxialing Mountains comprises the Poyang Lake water system of the Yangtze River basin and independent coastal rivers of eastern China, including the Qiantang River, Oujiang River, Minjiang River, and Hanjiang River. It is a key area for the conservation of biodiversity in Chinese ecosystems. In this study, fish surveys were conducted in 111 upstream sections of five river basins draining the Wuyi-Xianxialing Mountains and over 13,000 specimens were collected. The fish fauna of this area, on the basis of our investigations and records from historical literature, included 282 species, of which 239 were freshwater fishes, belonging to 101 genera, 23 families, and 6 orders. The orders of Cypriniformes, Perciformes, and Siluriformes supported the majority of fish composition in this area, with 181, 29, and 22 species, respectively, accounting for 75.73%, 12.13%, and 9.21% of total freshwater fish found. There were 109 fish species that were the major component of fish composition of the river plains of East Asia and 51 species of warm water fish with Southeast Asian origin, accounting for 45.61% and 21.34% of the total freshwater fishes, respectively. There were many species shared among the five river basins, and the average faunal resemblance of any two rivers was more than 50%. For the four substantive rivers in the eastern region, from north to south, the proportion of endemic fishes in the river plains of East Asia gradually decreased, and the proportion of warm water fishes of Southeast Asian origin gradually increased. Clustering analysis of fish fauna demonstrates that Poyang Lake, Qiantang River, Oujiang River, and Minjiang River are clustered into one class, while Hanjiang River forms the other class. This analysis indicates that the Wuyi-Xianxialing Mountains do not form a strong barrier for freshwater fishes, and that the whole district of the Wuyi-Xianxialing Mountains should be a component of the Oriental Region. In view of the differences between the north and the south, this paper argues that Hanjiang River in the southeast belongs to the South China Area of the South-east Asiatic Subregion, while Poyang Lake, Qiantang River, Oujiang River, and Minjiang River belong to the East China Area.