Characteristics important in identification of Heterocapsa species (i.e., thecal plate pattern, body scale structure, and shape and position of the nucleus and pyrenoid) are practically identical in the dinoflagellate investigated here and in Heterocapsa arctica T. Horig. described from the Canadian Arctic. Analysis of internal transcribed spacer (ITS) sequences confirms that the two dinoflagellates are very closely related; however, there is a clear difference in their size and shape. Our experiments show that the low-salinity Baltic Sea brackish water does not reduce the size of the marine H. arctica to match that of the Baltic Sea morphotype. On the basis of these dissimilarities in general morphology and its geographic isolation in the Baltic Sea, we consider our material sufficiently differentiated from the typical H. arctica to warrant the status of a new subspecies, H. arctica subsp. frigida subsp. nov. Being of a distinct cell shape, the occurrence of subsp. frigida has been recorded in Algaline phytoplankton monitoring data collected since 1993. Although it has never been responsible for high biomass blooms, it commonly occurs in spring in the Northern Baltic Proper and in the western Gulf of Finland, when the water temperatures are <5°C.