Microcystis panniformis is a bloom forming species with flat panniform-like colonies. This species was recently found in Lake Taihu, China. To specifically characterize M. panniformis based on isolated strains, morphological examination on colonial transition and genetic examination are needed. Three M. panniformis strains isolated from a water bloom sample in Lake Taihu were characterized by molecular analysis and toxin quantification. Phylogenetic analysis based on both 16S rRNA gene and internal transcribed spacer (ITS) between 16S and 23S rRNA genes were performed and compared to facilitate easy identification of the species. Relatively high similarities (98%-99%) were shown in 16S rDNA sequences between the strains of M. panniformis and those of other Microcystis species, whereas the similarities for ITS sequences were 88%-95%. In the phylogenetic tree based on the 16S rDNA sequences, the M. panniformis and M. aeruginosa strains were intermixed together with no clear division, whereas all of the M. panniformis strains were clustered together in a single clade based on the ITS sequences based phylogenyetic tree. The mcyE gene was detected in all three strains, and microcystin was determined by high-performance liquid chromatography. The molecular detection and toxin production of M. panniformis strains are of great significance for the environmental risk assessment of Microcystis blooms.