Abstract:As the last undammed tributary of the upper Yangtze River, Chishui River is an important protected aquatic habitat. There is a very close relationship between phytoplankton and the aquatic environment. Changes in phytoplankton composition and distribution are regularly used as indicators in environmental monitoring. Furthermore, phytoplankton community structure can be affected by changes in the environment. In this paper, the relationship between the phytoplankton community structure and aquatic environmental factors in the Chishui River was analyzed. Phytoplankton data and aquatic environmental factors were obtained from research investigations in the Chishui River National Nature Reserve for Rare and Endemic Fishes in the Upper Reaches of the Yangtze River during 2007 to 2010. The investigations were usually carried out each year in June, September and December. The investigations recorded 517 phytoplankton species belonging to eight phyla. Species of Chlorophyta and species accounted for 17.83% and 10.61%, respectively, while species totaled 1.98% and 1.34%, respectively. Phytoplankton species of accounted for 0.70%, 0.93% and 0.50%, respectively. Regarding phytoplankton density and biomass, to 28.31×104 cell·L, respectively, at the fish breeding stage. At the fish fattening stage, average value for density and biomass ranged from 10.32×104 to 33.73×104 cell·L, respectively, while at the wintering stage the average values ranged from 11.53×104 to 26.38×104 cell·L, respectively. For phytoplankton community biodiversity, the average Shannon–Wiener’s diversity index (J) were 4.42, 6.93 and 0.84, respectively. The community biodiversity results indicate that most sampling sites in the Chishui River were unpolluted, except for the Tucheng sampling site. The relationship between phytoplankton community structure and aquatic environmental factors was analyzed by canonical correlation analysis (CCA). The result of CCA indicated differences in the phytoplankton community structure at the three sampling stages. The aquatic environmental factors, including -N) and total nitrogen (TN), had a major influence on the phytoplankton community structure at the fish breeding stage,) was the main influencing factor at the fish fattening stage, while ) and water temperature (WT) were significant factors at the fish wintering stage.