To discriminate from toxic and non-toxic Microcystis, 3 pairs of primers epF/mb1R, mcF/teR and mcF/umR were designed, based on sequences of microcystin synthetase gene cluster. The primers were applied to test the toxicity of 19 strains of Microcystis, which came from different places, including China, America, Japan and Australia, via whole-cell PCR. All these primers, cpF/mb1R, mcF/teR and mcF/umR, were able to amplify the expected bands from 15 toxic strains of Microcystis. The amplified fragments were 2,800bp, 1,800bp, 2,300bp respectively. The bands were proved to be the fragments of microcystin synthetase gene cluster according to blasting the sequences datum of PCR products on NCBI. In addition, we compared the results by two methods of PCR and HPLC. It showed that both PCR and HPLC methods gave a similar result on toxicity of Microcystis strains, and indicated that 3 pairs of primers could distinguish between toxic and non-toxic Microcystis. To detect the sensitivity of the primers, the threshold of primers for cell concentration was also studied. The results showed that the optimal concentrations were from 2 x 105 cells/mL to I X 107 cells/mL. Especially, the primes mb1R/epF, mcF/umR could amplify the expected bands on the cells concentrations of from 2 X 104 cells/mL. It was concluded the 3 primers were highly sensitive,and able to apply for discrimination of toxic and non-toxic strains of Microcystis.