Abstract: To evaluate water quality of a wetland system, a comprehensive survey on the community structure of protozoan was carried out in the open area of the Xixi National Wetland Park of Hangzhou, southern China, from June to August, 2011. Protozoan samples were collected monthly at seven sampling stations with a spatial gradient of environmental status. Finally, a total of 21 protozoan samples were collected. Physicochemical parameters, including water temperature, pH, dissolved oxygen (DO), chemical oxygen demand (COD), biological oxygen demand (BOD5), total phosphorus (TP) and total nitrogen (TN), were measured according to the Water and Wastewater Monitoring and Analysis Methods for comparison of biological data. By using the freshwater plankton survey methodology, we investigated species composition, community characteristics, dominant species distribution, indicator species and biodiversity indexes of protozoan in Xixi Wetland. Identification was made mostly according to the morphology, mainly on the basis of the published books with protozoan pictures. Environmental and biological data were packed up and analyzed by EXCEL 2007 and SPSS13.0. Finally, a total of 84 species of protozoan were identified, belonging to 3 classes, 45 genera, with 61 flagellates, 14 ciliates, and 9 sarcodinas in the Xixi Wetland. Whether in the species number or abundance, flagellates a the largest proportion. A total of 8 dominant species were collected including Chilomonas ovalis, Cryptomonas erosa, Cryptomonas marssonii, Cryptomonas obovata, Cryptomonas ovate, Cryptomonas pyrenoidifera, Euglena caudate and Euglena proxima, which belong to flagellates. We found 15 pollution indicators including 3 heavy-polluted, 9 -medium-polluted, 8 -medium-polluted and 3 light-polluted indicators, in which medium-pollution indicators accounted for 86.67%, and Cryptomonas erosa, an -medium-pollution indicator, was also a dominate specie. The Simpson index and evenness index were a little low while Margalef index and Shannon-Wiener index were moderate, and all diversity indexes suggested that the water of Xixi National Wetland Park was slightly polluted. Among the seven sampling sites, there were no statistically significant differences in biotical data including species number, abundance and all diversity indices. In the functional nutrition taxa of protozoan, the photoautotrophic (P group) were significantly more than the other functional groups, with the majority of Cryptomonas and Euglena that liked to live in the organic- rich water. In all environmental data, the values of TN, TP and COD were higher and made a main effect to protozoan communities. The variation of species number kept significant negative correlation with the changes of T value and pH value, when significant positive correlation with the changes of COD value. The variation of Margalef index and Shannon-Weiner index kept significant negative correlation with the changes of pH value. These results should help us to understand more about the structures and functions of protozoan community in the Xixi Wetland. Both the environmental and biotical data suggested the water of the Xixi Wetland was slightly polluted and should be protected intensively. In summary, the protozoan communities showed a clear coordination in response to the environmental pressure, and they can be used as a robust tool in assessing water quality in freshwater wetland systems based on our research.