Abstract Two Gonyaulax-like strains were established by isolating cells from Korean coastal waters, and their morphologies and molecular phylogenies based on SSU and LSU rRNA gene sequences were examined. The motile cells displayed neutral torsion and a plate formula typical for the genus Gonyaulax, and were characterized by a reticulated surface with many pores, and a marked antapical flange on the boundary between 1″″ and 2p or two prominent spines. The reticulate ornamentation was sometimes absent on the plate margin or on the entire plate. Pronounced rows of pores on the margins of precingular, cingular and postcingular plates were observed, and especially a distinct pore was always present on the margin of the anterior sulcal plate contacting with 1″. A spiniferate resting cyst had a red body, gonal and intergonal processes, and an antapical flange. In the phylogenetic tree, the Korean isolates had a close relationship to Gonyaulax membranacea and were clearly divergent from other Gonyaulax species. These species can be distinguished by the presence or absence of a distinct pore on the margin of the anterior sulcal plate in touch with 1″, and different process types in cyst morphology. Based on these morpho-molecular data, Gonyaulax kunsanensis sp. nov. is proposed.