For characterization of Microcystis species and strains, cell size, growth temperature optimum, salinity tolerance, dark chemoheterotrophy, photoheterotrophy, guanine + cytosine content in DNA, total fatty acid composition and restriction fragment length polymorphism of a polymerase chain reaction product (PCR-RFLP) of the cpcBA intergenic spacer and flanking region were examined using 24 strains of Microcystis isolated from various lakes and ponds in Japan. From the results obtained it was observed that Microcystis spp. displayed low phenotypic diversity. Cell diameters of these strains were overlapping and there was no clear correlation with morphospecies. Slight differences in growth temperature optimum and salinity tolerance were observed among all strains. No strains showed either chemoheterotrophy or photoheterotrophy. The fatty acids present were the same in different strains although the amounts were different. All the strains had a similar G + C content ranging from 39 to 43 mol%. The phonogram constructed from the PCR-RFLP analysis showed that the species assignment for Microcystis species by morphology did not correspond with the genetic background.