The occurrence and distribution of microcystins were investigated in Lake Taihu, the third largest lake in China. An extensive survey, larger and broader in scale than previous studies, was conducted in summer 2010. The highest microcystin concentration was found at southern part of Taihu, which was newly included in this survey. In northern coastal areas, total cellular concentrations of 20 to 44 μg/L were observed. In northern offshore waters, levels were up to 4.8 μg/L. Microcystin occurrence was highly correlated with chemical oxygen demand, turbidity, and chlorophyll-a. Extracellular/total cellular microcystin (E/T) ratios were calculated and compared to other water quality parameters. A higher correlation was found using E/T ratios than original microcystin values. These results show that algal blooms are having a severe impact on Lake Taihu, and further and extensive monitoring and research are required to suppress blooms effectively.