AbstractWe synthesized the information on fish diversity in the Yangtze River Basin, documenting 378 species/subspecies that had been recorded and described from the basin, belonging to 14 orders, 32 families and 144 genera. Of these, 338 species/subspecies are freshwater fishes, of which 269 species/subspecies are from the Cypriniformes. Of the total, 11 species are migratory fishes, and 29 are species of brackish water of the estuary. A total of 162 species/subspecies are endemic to the river and 69 are threatened. We divided the Yangtze River Basin into 19 sub-basins. Except for the two sub-basins of the headwaters and the upper and middle reaches of Jinshajiang River, the other 17 sub-basins showed similar values in species richness and G-F diversity indices, although the values were higher in the upper reaches than in the middle and lower reaches. However, the proportion of endemic species decreased gradually from the headwater to the estuary of the basin in parallel with the gradient of elevation. Jaccard similarity analysis showed that the 19 sub-basins were clustered into three groups: (1) the headwaters and the upper and middle reaches of Jinshajiang River, located in the eastern Qinghai-Xizang Plateau and Hengduan Mountains; (2) the other sub-basins of the upper reaches, located in Western Sichuan Plateau, Yungui Plateau, Sichuan Basin, and Qinling-Daba Mountains; (3) the middle and lower reaches, belonging to the Huaiyang Mountains, Jiangnan Hills and the plain along the middle and lower reaches of the Yangtze River. This grouping reflects the environmental characteristics of the basins and the three large topographic plat-forms of the Chinese mainland.