Since the distribution patterns of amphibians are largely determined by the existence of water, we divided the Yangtze River Basin into 18 sub-basins according to the main tributaries. Based on the sub-basins, we synthesized information on amphibian biodiversity in the Yangtze River Basin. We documented 145 species that had been recorded and described from the basin. There are 2 orders, 10 families and 30 genera. Of these, 49 and 69 species are endemic and threatened, respectively. Except two sub-basins at the highest elevation in the basin, the headwater, and the upper and middle of Jinshajiang sub-basin, the other 16 sub-basins show a decreasing tendency in species richness and threatened species richness from the headwater to the estuary. Moreover, the proportion of endemic species decreased gradually from the headwater to the estuary of the basin with a gradient of the elevation. By calculating the G-F diversity index of the 18 sub-basins, the G index was found to reflect the species richness, and F index and G-F index showed similar values among the sub-basins except for three sub-basins of the headwater, Hanjiang and Ganjiang. Based on the species distribution (Jaccard similarity), cluster analysis was used to analyze the similarity of amphibians in 18 sub-basins. The sub-basins were clustered into six groups: (1) the headwater, (2) Hengduanshan Ranges, (3) Yun-Gui Plateau, (4) Eastern West Sichuan Plateau, Sichuan Basin, and Qinling-Dabashan Mountains, (5) Dongting Lake and its tributaries, Poyang Lake and lower reaches of the basin, and (6) Ganjiang sub-basin. The grouping result reflects to the environmental characteristics of the total basin and three large topographic platforms of the Chinese mainland.