To evaluate the public health risk of exposure to microcystins in fish food in China, the distribution pattern of microcystin-LR and microcystin-RR in various organs (liver, intestine, kidney, muscle and lipid) of the dominant freshwater phytoplanktivorous fish Hypophthalmichthys molitrix in Hangzhou, China's Tiesha River was investigated with the method of HPLC-ESI-MS analysis. The distribution of microcystins was different in the fish organs and the major total microcystins (microcystin-LR and microcystin-RR) were present in the intestines (6.49 μg/g fresh weight), followed by the livers (4.52 μg/g fresh weight) and the muscles (2.86 μg/g fresh weight). Microcystins were detected in kidneys (1.35 μg/g fresh weight), but not detected in lipid. The results suggested that the mean daily intake from fish was 0.03 μg/kg body weight which was very close to the recommended WHO tolerable daily intake (TDI) level of 0.04 μg/kg body weight per day, and local people were warned they may have health risk if they consumed fish from the river.