Abstract: Toxic Microcystis could produce heptapeptide toxins called microcystin which may do harm to human body, and then a nested PCR was developed for the detection of toxic Microcystis in water samples from reservoirs. Two specific nested pairs of primers were designed from the partial sequence of microcystin synthetase gene B ( mcyB). The results of detection by nested PCR were consisted with those by conventional ELISA method, which could be used to measure the concentration of microcystin of different water bodies. Detection results of some water samples were negative by ELISA method with 50 mL reservoir water (sensitity Microcystis. The sensitivity of the nested PCR2mediated detection of mcyB was up to 1-10 cells per reaction. This nested PCR was used to detect water samples from 12 supply water reservoirs in Guangdong Province. The 247 samples, collected from March 2003 to December 2004, were estimated by nested PCR method. Eighty-two positive samples were detected by nested PCR and the total positive ratio was 33.2 %. Positive samples were detected by nested PCR from all the reservoirs except for the Shenzhen Reservoir. The PCR positive ratio of water samples from the Tangxi Reservoir was 67.4 %, which was the highest among all the reservoirs and that of one step PCR was 25.6 %. Thus this reservoir should be paid more attention to in the future.