Abstract: The present study surveyed the distribution of microcystin-producing gene-mcyB by PCR among 38 bloom-forming cyanobacterial strains from FACHB-Collection. The results demonstrated that special amplifications were being gotten only from 19 toxic Microcystis strains, whereas it was deficient in nontoxic ones got none. The PCR results showed highly agreement with the toxicity of every strain determined by HPLC, ELISA, and Bioassay respectively. Furthermore, the traditional PCR protocols were simplified by checking the cyanobacteria cells directly instead of the previously used extracted genomic DNA. The whole cells PCR we developed in this study could be successfully applied to cultured algae materials, water samples and lyophilized cyanobacterial cells. Thus, discrimination of toxic and nontoxic Microcystis strains by molecular biological technologies proves to be practicable and efficacious.