Scrippsiella trifida Lewis, 1991 ex Head, 1996 is a nontoxic marine calciodinelloidean dinoflagellate whose resting cyst has a distinctive wall containing large, erect, trifurcate, recurving calcareous processes that separate two organic layers. We show that the organic wall layers of living Scrippsiella trifida cysts are resistant to acetolysis and can therefore potentially fossilize, and we report on abundant Scrippsiella trifida cysts from latest Pleistocene and early Holocene marine sediments off eastern Canada, representing the first confirmed fossil discovery of this species in the North Atlantic. A reappraisal of late Quaternary palynological records now shows that the organic remains of Scrippsiella trifida cysts have been widely misidentified as cysts of Alexandrium tamarense (Lebour, 1925) Balech, 1985, a goniodomacean (and hence noncalcareous) dinoflagellate and major cause of paralytic shellfish poisoning in humans. The morphology of these two cyst types is contrasted, and the modern and fossil distribution of Scrippsiella trifida cysts in sediments of the North Atlantic and adjacent areas is now clarified. It is apparent from this distribution that Scrippsiella trifida favors neritic environments characterized by cool winters and relatively warm (14°–25°C) summers. Extremely high fluxes of S. trifida cysts in nearshore areas off Nova Scotia and southern Greenland during deglaciation and early postglacial time (14–7 ka) have no modern analog but may signal a reduction in salinity caused by meltwater discharge. In general, the organic walls of calcareous dinoflagellate cysts are more common components of palynological assemblages than hitherto realized.