Microcystis aeruginosa is common form of cyanobacteria (blue-green algae) capable of producing toxic heptapeptide (microcystin) that cause illness or death. The comparison of molecular genetic method with the morphological characteristics of cyanobacteria was conducted. We have designed PCR primers (JJM98F, JJM1141R) for cyanobacterial 16S rRNA and phycocyanin intergenic spacer (PC-IGS) gene domain. To confirm the production of microcystins, PCR primers for the N-methyltransferase (NMT) domain of microcystin synthetase gene mcyA were designed using 21 cyanobacteria strains Most of isolated strains from the Nakdong River was classified as Microcystis aeruginosa and the similarities were $99\%$ with M. aeruginosa AF 139292. $38.1\%$ of isolated strains contained microcystin synthesis gene. NMT (N-methyltransferase) were not detected in isolated strain in several strains, which means non-toxic. However, the NMTs of the strains were detected during the cultivation.