In order to document the distribution of dinoflagellate cyst assemblages, eight surface sediment samples were collected in surface sediments from southwestern Black Sea and Canakkale Strait. A total of 25 cyst types and 1 unknown cyst type were identified. Samples displays low total cyst concentrations with values ranging from 8 to 346 cyst g(-1) dry weight sediment. Autotrophic dinoflagellates highly and significantly contributes (p<0.01) to the total cyst concentration. Lingulodinium machaerophorum, cyst type of Alexandrium minutum and Spiniferites bulloideus were dominant at the sampling points. Higher cyst concentration and diversity observed at stations in Black Sea could be linked to the type of sediment. Small-sized sediment (sand-silt) were mostly dominant at the Black Sea stations compare to the more sandy type sediment of Canakkale Strait. Present study provides the first modern dinoflagellate cyst records from surface sediments of southwestern Black Sea and Canakkale Strait.