Abstract: Colonial Microcystis aeruginosa isolated from water-bloom of Dianchi Lake lost its colonial type and became single-celled type upon continuous subcultured in inorganic medium. It was observed that the growth rate of colonial M.aeruginosa was markedly lower than that of single cell; the extracellular acid polysaccharide capsule was obviously visible in the colonial type but was absent in the single-celled one; toxin analysis indicated that three microcystins isomers were produced in colonial M. aeruginosa, but in single-celled M. aeruginosa, only one major toxin-MC-LR was detected; sing celled M. aeruginosa had the LD 50 value almost ten times higher than colonial M. aeruginosa. Allozyme divergence was detected, too. The study has brought forward a new proof to explanation of mechanisms on regulation of microcystin synthesis.