Abstract: Abstract：In the large high-productive river basin, periphytic algae are the base of the food web for many organisms in the natural ecosystem, and now have been played an important role in monitoring the water quality and assessing the health of aquatic ecosystem in order to manage the river watershed. In the present study, the structure of periphytic algae community and its relationship with water environmental factors were explored throughout the Ganjiang River basin, the largest river in Jiangxi. Fifty-three sampling sites were chosen for the investigation of the periphytic algae community in Ganjiang River during the high water period. Results showed that a total of 175 periphytic algaespecies were identified in Ganjiang River, belonging to 42 genera of 3 phyla. There were 151 species of Bacillariophyta, 12 species of Chlorophyta and 12 species of Cyanophyta in the river, respectively. Navicula was the dominant genus in Ganjiang River basin, occupied 14.080% of periphytic algae genera density. Cymbella and Navicula were the dominant genus in the downstream of Ganjiang River basin, occupied 13.088% and 12.935% of the genera density, respectively. Cymbella was the dominant genus in the midstream, occupied 12.849% of the genera density. Gomphonema was the dominant genus in the upstream, occupied 10.150% of the genera density. The Monte Carlo significance test results showed that the periphytic algae in downstream was significance affected by total nitrogen (TN), dissolved oxygen (DO), Chlorophyll a and conductivity. The periphytic algae in r midstream was significance affected by altitude, velocity, river width, and total phosphorus (TP). The periphytic algae in upstream was significance affected by TN, river width, turbidity and velocity. Redundancy analysis (RDA) was applied to reveal the relationship between periphytic algae community and water environmental factors. Results showed that Chlorophyll a and conductivity were the main factors for periphytic algae communities in the downstream. Altitude and TN were the main factors for periphytic algae communities in the midstream and upstream, respectively. It could be suggested that the water quality was reflected by the community structure of periphytic algae to some extent in the downstream and upstream, but not for the midstream.