The principle organization of microcystin biosynthesis (mcy) gene clusters is characterized in three genera among the microcystin-producing cyanobacteria. To examine the conservation of the mcy gene clusters among the genus Microcystis, internal non-coding regions of the cluster in 21 strains including M. aeruginosa, M. viridis, and M. wesenbergii, were amplified by PCR using specific primer sets and sequenced. PCR-based analysis revealed a completely conserved organization of the bidirectional cluster structure, mcyABC and mcyDEFGHIJ, among all toxic and some microcystin-negative strains. Furthermore, all mcy gene clusters were flanked by a gene with homology to dnaN adjacent to mcyJ and by uma1 with no-homology to any known genes at the 3'-end of mcyC. Transposase homolog genes were observed in a non-coding region between dnaN and mcyJ in three microcystin-producing Microcystis strains. Sequence analysis of a region adjacent to uma1 in mcy-negative strains revealed two types of gene constitution, dnaN-uma1 and the hypothetical protein gene-uma1. PCR-based analyses can be used to assess the identification of microcystin-producer strains in Microcystis spp.Key words: Cyanobacteria, Microcystis, Microcystin biosynthetic gene, Non-ribosomal peptide synthetase, Polyketide synthase Noxious cyanobacterial waterblooms are occurring worldwide in eutrophic lakes, ponds, and dams. Members of the genus Microcystis, a major cause of freshwater blooms, can be toxic. Microcystins, a family of cyclic heptapeptide toxins that are produced by most members of this genus, cause acute hepatotoxicity in agricultural livestock 1,38) . The toxicity of microcystins is due to the inhibition of protein phosphatase 1 and 2A 8,16) . The increasing occurrence of Microcystis blooms in sources of human drinking water is very problematic 5) .Microcystins share a common structure, cyclo (Adda-D-, in which X and Z are variable L-amino acids, Adda is 3-amino-9-methoxy-2,6,8-trimethyl-10-phenyldeca-4,6-dienoic acid, D-MeAsp is D-erythro-β-iso-aspartic acid, and Mdha is N-methyldehydroalanine. Peptides containing non-proteinogenic amino acids are synthesized by non-ribosomal peptide synthetases (NRPSs), which are a family of multifunctional enzymes 9) . NRPSs are composed of modules, each of which is responsible for the activation of an amino acid, thiolation, and condensation 9) . Notably, epimerization and methylation occurred the NRPS module in order to modify the amino acid. Recently, microcystin synthetase genes have been cloned and sequenced from the microcystin-LR type producer Microcystis aeruginosa 17,18,35) , which produces heptapeptide micropeptin/cyanopeptolin as well 4,10) . The mcy-ABC cluster has the opposite orientation to the mcyDEFG cluster 18,35) . Additionally, monofunctional proteins for