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Blooms of cyanobacteria are an increasingly frequent phenomenon in freshwater ecosystems worldwide as a result of eutrophication. Many species can produce hepatotoxins that cause severe health hazards to humans. The aim of this study was to identify the bloom forming cyanobacteria species by molecular methods and to amplify genes responsible for hepatotoxin biosynthesis from the environmental samples and isolated strains of cyanobacteria from Küçükçekmece Lagoon, Sapanca, İznik, Manyas and Taşkısı Lakes. A total of 10 bloom samples and 11 isolated strains were examined and Microcystis spp., Planktothrix spp., Nodularia spumigena, Anabaenopsis elenkinii, Sphaerospermopsis aphanizomenoides, Cylindrospermopsis raciborskii were identified. Hepatotoxin genes were detected in 60% of the bloom samples and 45% of the strains. Two Microcystis strains were obtained from Küçükçekmece Lagoon. While the strain assigned to Microcystis flosaquae was non-toxic, Microcystis aeruginosa strain produced microcystin. According to PCR results, the M. aeruginosa and Planktothrix agardhii bloom samples of Küçükçekmece Lagoon contained the microcystin synthetase gene E (mcyE) indicative of microcystin production, however, no microcystin was detected by HPLC. The mcyE gene was also found in Microcystis wesenbergii isolated from Taşkısı Lake, and in all Planktothrix rubescens bloom samples from Sapanca Lake. To our knowledge, this is the first detailed study for identifiying different toxic cyanobacteria species and their hepatotoxin production from several waterbodies in Turkey using molecular methods.