Thirty-four dinoflagellate cyst taxa were found in surface sediment (0-2 cm) at five stations (60-100-m water depth) in the Gulf of Gemlik, Marmara Sea, during four seasons from August 2011 to May 2012. Lingulodinium machaerophorum, Operculodinium centrocarpum and Selenopemphix quanta dominated cyst assemblages in the polluted gulf, where nutrient-rich surface water was stratified during most seasons and bottom water was hypoxic. Twelve cyst taxa were incubated and produced motile cells that reproduced and survived 14-15 days. Highest cyst species number (33) occurred in summer; maximum number of cysts (living and empty) per cm 3 wet sediment was in spring, with the annual range from 1520 (fall) to 108,000 (spring). Nine taxa (Brigantedinium simplex, L. machaerophorum, O. centrocarpum, S. quanta, Spiniferites mirabilis, Spiniferites ramosus, cysts of Alexandrium sp., Scrippsiella trifida and S. trochoidea) were found in all seasons at all stations. The harmful dinoflagellates L. machaerophorum and cysts of S. trochoidea and Alexandrium sp. were the most abundant species. The cyst of the toxic species, Cochlodinium sp., is reported for the first time from Turkey. Other HAB species included A. tamarense, Protoceratium reticulatum, Heterocapsa triquetra and Gymnodinium catenatum/nolleri. Relative abundance of potentially toxic dinoflagellates (74%-92% of total cysts cm(-3)) was always higher than nontoxic species, and percentage abundance of cysts cm(-3) produced by autotrophs (19/34 total species) almost always exceeded those of heterotrophs. Although distributions of the resting cyst taxa were significantly influenced by surface temperature, dissolved oxygen and total water depth, surface salinity was the strongest predictor for cyst occurrences.