The distribution of calcareous dinoflagellate cysts in surface sediments from the Mediterranean Sea was quantitatively analysed. The samples contain 11 cyst species and the vegetative coccoid Thoracosphaera heimii. Cyst abundance increases towards the deeper parts of the basins and is generally higher in the eastern Mediterranean Sea. Three major distribution characteristics exist: (1) different assemblages in oceanic and neritic regions, (2) little agreement with the associations of areas studied so far like the Atlantic Ocean, and (3) a unique oceanic assemblage in the eastern Mediterranean Sea. A gradual change in cyst assemblages from the western to the eastern Mediterranean Sea was observed and statistically compared with the main environmental gradients in the upper water column. Temperature, nitrate concentration and possibly salinity appear to be the most important factors controlling cyst production. Three groups containing cysts with similar environmental preferences can be distinguished: (1) an eastern Mediterranean group related to relatively high temperature and salinity but low nitrate concentration, (2) a group of more or less consistently abundant cosmopolitan species tolerating or even preferring relatively low temperature and salinity but high nitrate concentration, and (3) a group containing species that are possibly adapted to neritic environments and have probably been transported from coastal areas into the studied regions. In contrast to other calcareous plankton, calcareous dinoflagellate cysts correlate strongly with the main environmental gradients in the Mediterranean Sea, bearing a high potential for palaeoenvironmental reconstructions.