Abstract: As a part of the molecular taxonomic revision of the genus Microcystis (Cyanophyceae), genome DNA divergence within and between three Microcystis species including seven strains from different areas were analyzed electrophoretically after using randomly amplified polymorphic DNA PCR with 24 primers.The main result was summarized as follows: (1)the genus Microcystis includes at least four taxonomic entities which differ in morphology and genetics: M.aeruginosa 101, M.aeruginosa 7820, M.aeruginosa 90 and M sp.( Dianshan) ; M.viridis ; M.wesenbergii; M.aeruginosa.41.(2) M.aeruginosa comprises two heterogeneous taxonomic entities which could be viewed as separete species.(3) for their unique genotype and minor morphological variation, M.viridis and M.wesenbergii are regarded as well-established species.(4)as anticipated, Anabaena sp 7120 as the control exhibits entirely different genotype and farther genetic distance than those of other Microcystis strains.The RAPD study on the genus Microcystis illustrates that it is possible to analyze intra- and inter-specific variation of Cyanophytes on the basis of genotype rather than phenotype and, therefore, offers significant and indispensable clues in solving taxonomic problems of cyanophytes, especially at the species and genus levels.Combined with the on-going research on special primers which sensitively and reliably distinguish the toxic and non- toxic strains of Microcystis, RAPD would be a helpful method to understand more explicitly the phylogenetic relationships between toxic and non-toxic strains of the genus Microcystis.