This paper analyzed the distribution and variation of microcystin(MC) and physicochemical factors in Macun and Haidong bay of Dianchi Lake from April to December in 2003. The correlation of some physiochemical factors, including the concentration of total nitrogen, total phosphorous, dissolve oxygen, chlorophyll-a and Seechi depth, light intensity, pH, water temperature and dominance of Microcystis population, with microcystin was evaluated. Correlation analysis showed that the distribution of MC was significantly positive correlated with TN and N-P (P<0.01); and affected by Seechi depth, light intensity, dominance of Microcystis (P<0.05). Multiple continuously factors analysis indicated that the distribution of MC in water of the two bays was mainly afferled by total nitrogen,Seechi depth, chlorophyll-a, dissolve oxygen and total phosphorous (R²=0.560,P<0.017).