The aim of this study was to identify dinoflagellate species from the Black Sea (Samsun coast) using conventional and molecular phylogenetic methods. Water samples were collected using a plankton net with 22 µm pores. Dinoflagellate cells were documented under a light microscope and were then isolated for the single-cell PCR procedure. Phylogenetic inference showed that the isolates collected from the study area were affiliated with various harmful taxa: Dinophysis acuta Ehrenberg and Phalacroma rotundatum (Claparéde & Lachmann) Kofoid & Michener from dinophysioids, and Prorocentrum compressum (Bailey) Abé ex Dodge, P. cordatum (Ostenfeld) Dodge, and P. micans Ehrenberg from prorocentroids. In the phylogenetic tree we also observed that 2 of our gymnodiniod isolates were in a deep branch, indicating a cryptic genus of the family Kareniaceae. One of our isolates was related to the genus