In present study, partial sequences (9746p) of gyrB gene of 7 strains of M.oeruginosa and I strain of M.flos-aquoefrom Lake Taihu(Jiangsu Province) and Tangxi Reservoir(Guangdong Province)respectively were measured,and 40 variablepoints and 17 parsimony informative sites were found. The mean parameter of (G+C) %was 47.8 %, and the sequence similarityamong them were more than 97.10%.In the Neighbor-Joining Tree, different moqhorspecies were intertwined and could not bediscriminated clearly, indicating that genotypes clustering ha no directly relations to phenotypes. The different geo graphical strainsdidn't clustered together either, indicating that geographic differences didn't affect genetic similarity,and supporting the taxonomictreatment that different species he classified as Microcystis aeruginosn complex-species temporarily.The resolution effect of gyrBgene to genetic diversity of Microcystis was better than 16S rRNA, and was similar to 16S-23S ITS and cpcBA-IGS, suggestingthat gyrB gene may be a good molecular marker in studying the taxonomy and genetic variation of Microcystis.