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The total dinoflagellate cyst community and the cysts of  Cochlodinium polykrikoides  in the surface sediments of South Sea (Tongyeong coast), South Korea, were analysed using next-generation sequencing (NGS) and morphological approaches. Dinoflagellate cysts can be highly abundant (111–4,087 cysts g −1  dry weight) and have diverse species composition. A total of 35 taxa of dinoflagellate cysts representing 16 genera, 21 species (including four unconfirmed species), and 14 complex species were identified by NGS analysis. Cysts of  Scrippsiella  spp (mostly  Scrippsiella trochoidea ) were the most dominant and  Polykrikos schwartzii ,  Pentapharsodinium dalei ,  Ensiculifera carinata , and  Alexandrium catenella/tamarense  were common. Thus, a combination of NGS and morphological analysis is effective for studying the cyst communities present in a given environment. Although  C. polykrikoides  developed massive blooms during 2013–2014, microscopy revealed low density of their cysts, whereas no cysts were detected by NGS. However, the vegetative  C. polykrikoides  not appeared during 2015–2017 in spite of the observation of  C. polykrikoides  cysts. This suggests that the  C. polykrikoides  blooms were not due to development of their cysts but to other factors such as currents transporting them to a marine environment suitable for their growth.

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Mapping distribution of cysts of recent dinoflagellate and Cochlodinium polykrikoides using next-generation sequencing and morphological approaches in South Sea, Korea