Samples were collected from planktonic habitats of the fresh and brackish waters in Korea from August 2016 to May 2018. As a result, three genera and nine species were newly recorded in Korea. The unrecorded indigenous genera were Anathece, Chondrocystis and Geminocystis, and nine species were Anabaenopsis arnoldii, Anathece smithii, Chondrocystis dermochroa, Coelosphaerium aerugineum, Eucapsis microscopica, Geminocystis herdmanii, Microcystis panniformis, Synechococcus nidulans and Woronichinia karelica. Anathece smithii, Coelosphaerium aerugineum, Eucapsis microscopica, Microcystis panniformis and Synechococcus nidulans had been reported to inhabit freshwater, but these were found in brackish water in this study. Microcystis panniformis, which is a potential genus for causing green-tide, is taxonomically valuable in Korea.