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 mu m 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 (Claparede & Lachmann) Kofoid & Michener from dinophysioids, and Prorocentrum compressum (Bailey) Abe 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 Peridiniella Kofoid & Michener of an uncertain family in Gonyaulacales. Network analyses of the DNA sequences were performed for phylogeographic investigation of the isolates. Five isolates are related to potentially harmful algal species. We have reported the first molecular data concerning these potentially harmful species from the Black Sea.