Abstract:In order to understand the toxin characteristics and ITS sequences diversity of Microcystis in Guangdong reservoirs, twenty-eight Microcystis strains were isolated, and their toxin characters and ITS sequences obtained from fifteen Microcystis strains were analyzed. The results showed that microcystin-producing genotypes were dominated in Guangdong reservoirs by HPLC and PCR method of microcystin synthase gene (mcyE), and the main type of microcystin was MC-RR. ITS sequences of Microcystis strains from Guangdong reservoirs had more than 93.2% similarity. Neighbour-joining (NJ) tree indicated that different species and origin from different regions could gather in a group, and toxic and non-toxic strains could not be separated. It was suggested that genetic diversity of Microcystis strains in Guangdong reservoirs was low, and there were no correlation between ITS sequences and the presence of mcyE. Furthermore, phenotypes of Microcystis strains did not necessarily reflect their phylogeny. So the combination of traditional and molecular approaches required to reassess the current cyanobacterial taxonomy should become the focus in the future.