Aims: The aims of present study were to evaluate the abundances, genetic diversity of total and microcystin-producing Microcystis over temporal and spatial scales, and to investigate relationships among Microcystis and water parameters in Tai and Yang-cheng lakes. Methods and Results: Abundances of total and microcystin-producing Microcystis varied across sampling periods and locations, which were assessed using qPCR with primers specific to Microcystis 16S rDNA and mcyA genes. The 16S rDNA from two lakes were relatively diverse. However, mcyA genes were rather conservative and were >97% identical to reference sequences. The highly positive correlations between mcyA and microcystin presence (r=0 center dot 671 in Tai; r=0 center dot 799 in Yang-cheng) suggested that mcyA can be used as a good biomarker for microcystin productions. Conclusion: The results demonstrated that Microcystis were genetically diverse between these conjunctive lakes; however, mcyA genes were relatively conservative in two lakes. Quantifying mcyA by qPCR was an efficient tool for monitoring toxic Microcystis. Significance and Impact of the Study: This study has improved our understanding of observable differences within and between each lake on spatial and temporal scales. And the discovery of new mcyA sequences in natural water enriched the understanding of phylogenetic diversity of Microcystis and toxin-production-related mcy gene.