Abstract: In this study, thirteen strains of Planktothrix agardhii from the freshwaters in different provinces were examined to detect the sequences of the synthetase genes of microcystins, including mcyA, mcyE and mcyT. The PCR results showed that only mcyT gene was amplified in these strains, indicating that these strains are not microcystin producers. The phylogenetic analysis based on the mcyT gene demonstrated that the Planktothrix strains were divided into two clades in the Neighbor-Joining tree, well corresponding to the non-toxic and toxic strains, and the minimum similarity of the two clades were 98.5% and 99.1%. The results provided a new insight into the molecular divergence between toxic and non-toxic Planktothrix strains.