A naked dinoflagellate with a unique arrangement of chloroplasts in the center of the cell was isolated from the northern Baltic proper during a spring dinoflagellate bloom (March 2005). Morphological, ultrastructural, and molecular analyses revealed this dinoflagellate to be undescribed and belonging to the genus Gymnodinium F. Stein. Gymnodinium corollarium A. M. Sundström, Kremp et Daugbjerg sp. nov. possesses features typical of Gymnodinium sensu stricto, such as nuclear chambers and an apical groove running in a counterclockwise direction around the apex. Phylogenetic analyses based on partial nuclear-encoded LSU rDNA sequences place the species in close proximity to G. aureolum, but significant genetic distance, together with distinct morphological features, such as the position of chloroplasts, clearly justifies separation from this species. Temperature and salinity experiments revealed a preference of G. corollarium for low salinities and temperatures, confirming it to be a cold-water species well adapted to the brackish water conditions in the Baltic Sea. At nitrogen-deplete conditions, G. corollarium cultures produced small, slightly oval cysts resembling a previously unidentified cyst type commonly found in sediment trap samples collected from the northern and central open Baltic Sea. Based on LSU rDNA comparison, these cysts were assigned to G. corollarium. The cysts have been observed in many parts of the Baltic Sea, indicating the ecologic versatility of the species and its importance for the Baltic ecosystem.