Five surveys were carried on in Huizhou segment of Dongjiang River from 2007 to 2010. Total of 69 freshwater fish species belong to 8 orders, 20 families and 58 genera were collected, most of fishes belong to family Cyorinidae (39 species), Bagridae (7) and Cobitidae (5). Cirrhina molitorella, Hemiculter leucisculus, Cyprinus carpio and Squaliobarbus curriculus are dominated species in the lower reaches studied.Besides Gambusia affinis, four more exotic species including Tilapia sp., Labeo rohita, Cirrhina mrigala, and Hypostomus plecostomus were newly recorded.Compared with the data collected in 1980s’, the proportion of sedentary and omnivore species increased, while migratory and carnivore species declined.The result by using autecology matrix analysis showed that carnivore fish species living at gravel bottom and in riffle at downstream decreased greatly.According to Simpson index, Shannon-Wiener index, Pielou’s index, Margalef index and G-F index, the differences in fish community diversity in the up and down of Jiantan Dam was found.The important factors influencing the change of fish community in the lower reaches of the Dongjiang River might be the dam construction, water pollution, and excessive catching.