We isolated and purified a Microcystis strain, Chaohu-1, from Chaohu Lake by the method of plate streaking and liquid culture. After the successive steps of methanol extraction and solid-phase ex-traction, it was confirmed that the algae strain produces MC-LR as analyzed by HPLC. The algae cells were green and spherical, while the population displayed a random reticulate form. The phycocyanin intergenic spacer region (PC-IGS) was amplified by whole-cell PCR, cloned and sequenced. The PC-IGS sequence showed a degree of similarity of 99% with those of Microcystic aeruginosa strains downloaded from GenBank. A combination of the analysis results both at morphological and molecular levels indicated that for the first time we have isolated a Microcystis aeruginosa strain in Chaohu Lake, and we named it Chaohu-1. Moreover, we established an effective method for its cryopreservation and cell resuscitation, which laid foundation for the long-term preservation and the future research.