The relationship between the diversity of protozoan community and water quality in ponds for the culture of Siniperca chuatsi was studied through the detection of pond water physicochemical factors and the observation of plolyurethane foam unit（PFU） protozoan community. The experiment was conducted from September to November in 2004 at Shunde, Guangdong Province. Water physicochemical factors were determined by common method and water quality index was constructed according to GB3838 - 88. Protozoan samples were collected by PFU method and protozoan community diversity index was calculated by Margalef formula. The results showed that some factors such as TN （ NH4 - N, NO2 - N and NO3 - N） and chemical oxygen demand （COD） increased gradually as cultivation progressed. The results also showed that the water quality index increased in cultivation progress. The opposite trend was observed for the diversity of protozoan community. The water quality index and protozoa community diversity index can he used for evaluating water quality. The relationship between PFU protozoan community diversity index（y） and water quality index（ x ） could be expressed by y = 2.45 - 2. 54Inx, that is to say, the higher water quality index is, the lower the protozoan community diversity index is. Through correlation and regression analysis, coefficient of correlation and regression is significant at 0.01 level. It is also found that there is a relationship between protozoan community diversity index and S. chuatsi diseases. Protozoan community diversity index would become a good biofactor for prediction of S. chuatsi diseases.