Taihu Lake is the third largest freshwater lake in China. In recent years, the water pollution of cyanobacteria blooms has become a severe problem in this area. Microcystins (MCs) are an important group of toxic compounds mainly produced by some cyanobacteria species and have both acute and chronic hepatotoxic effects on animals and humans. This paper presents the first data on the identification and detection of MCs in both natural occurring cyanobacteria blooms and surface water samples (0-0.5 m), collected from Meiliang Bay, Taihu Lake, China. A conventional method for extraction and isolation of MCs from cyanobacteria blooms was applied. High-performance liquid chromatography (HPLC) analysis showed that the main toxic component in the cyanobacteria materials was MC-LR. The monoclonal antibody (mAb) against MC-LR produced by hybridoma technique was employed for direct competitive ELISA to detect the concentrations of MCs in bloom and water samples collected in 2001. The results not only revealed the presence of MCs but also temporal variations of MCs levels of three sampling stations in Meiliang Bay in 1 year. It is obvious that the MC contents were relatively higher during warm months and related with the status of eutrophication. Our study indicates the threat associated with MCs in water body of Taihu Lake. To prevent the MCs potential hazard on public health in this area, some necessary measures of monitoring and control of growth of cyanobacteria are urgently needed.