The first data on the distribution of microcystin genes among natural populations of different species of Microcystis from Russian reservoirs were obtained. It was statistically established that the occurrence of mcy gene-containing colonies of M. aeruginosa, M. viridis, and M. novacekii was significantly higher than that of M. wesenbergii and M. flos-aquae. It has been shown that M. wesenbergii from the water bodies in Russia and Eurasia is not capable of producing microcystins. These results are discussed with respect to various mechanisms that could explain the distribution of microcystin genes among the various Microcystis morphospecies, such as the compensation of microcystin functions by the synthesis of other secondary oligopeptides and the presence of dense mucilaginous envelopes surrounding the colonies of M. wesenbergii. No correlation was found between colony size and the frequency of mcy genes for individual morphospecies M. aeruginosa and M. flos-aquae.