There is increasing recognition that protozoa is very useful in monitoring and evaluating water ecological healthy and quality. In order to study the relationship between structure and function of protozoan communities and water qualities, six sampling stations were set on Lake Donghu, a hypereutrophic subtropical Chinese lake. Microbial communities and protists sampling from the six stations was conducted by PFU (Polyurethane foam unit) method. Species number (S), diversity index (DI), percentage of phytomastigophra, community pollution value (CPV), community similarity and heterophy index (HI) were mensurated. The measured indicators of water quality included total phosphorus (TP), dissolved oxygen (DO), Chemical oxygen demand (COD), NH 4 + , NO 2 − and NO 3 − . Every month water samples from stations I, II, III, IV were chemically analyzed for a whole year, Among the chemically analyzed stations, station I was the most heavily polluted, station II was the next, stations III and IV had similar pollution degrees. The variable tendencies of COD, TP, NH 3 , NO 2 − , NO 3 − , and DO during the year was approximately coincident among the six stations. Analysis from the community parameters showed that the pollution of station 0 was much more serious than others, and station V was the most slight. Of the community parameters, CPV and HI were sensitive in reflecting the variables of the water quality. Community similarity index was also sensitive in dividing water qualities and the water quality status of different stations could be correctly classified by the cluster analysis. DI could reflect the tendency of water quality gradient, species number and percentage of Phytomastigophora was not obvious in indicating the water quality gradient.