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. | Turkish Journal of Botany Turk J Bot (2016) 40: 546-556 © TÜBİTAK doi: Research Article First molecular records of potentially harmful planktonic dinoflagellates from the southern Black Sea 1 2, 1 1 1 Özgür BAYTUT , Cem Tolga GÜRKANLI *, Eda DENİZ , İbrahim ÖZKOÇ , Arif GÖNÜLOL Department of Biology, Faculty of Arts and Science, Ondokuz Mayıs University, Atakum, Samsun, Turkey 2 Department of Fisheries Technology Engineering, Fatsa Faculty of Marine Sciences, Ordu University, Fatsa, Ordu, Turkey 1 Received: Accepted/Published Online: Final Version: Abstract: 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 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. Key words: Black Sea, harmful dinoflagellates, phylogenetics, phylogeography, .