In the study, four methods used for quantification of cyanobacteria and Microcystis by SYBR Green I real-time quantitative PCR (RT-qPCR) were established based on the target genes, including the 16S rRNA gene of cyanobacteria, the phycocyanin and the 16S rRNA gene of Microcystis. Then the cultured M. aeruginosa and the environmental samples of Lake Taihu were evaluated by the established methods. Comparison between the new approaches and microscope counting indicated that RT-qPCR analysis could meet the requirement of algae bloom quantification and it was convenient, rapid and specific.