The zoogeography and systematics of the Mysis relicta species group were elucidated in an allozyme survey of populations across northern Europe and North America. The North American populations are here identified as an independent species (sp. IV), distinct from the three previously recognized European M. relicta group taxa (spp. I–III). The geographical pattern of gene frequency variation in North America supports a late-glacial colonization by separate eastern and western refugial stocks of sp. IV. In Europe, sp. III is known from a single subarctic lake, while both spp. I and II are widespread. They coexist in the Baltic Sea, but their lacustrine distributions are largely different. Species I accounts for most Fennoscandian populations and those in Poland and Germany whereas sp. II lives in Ireland, parts of southwestern Scandinavia, and Karelia. With the paleohydrographical reference, the distributions suggest that both species survived the last glaciation in proglacial lakes east of the Scandinavian Ice. Subsequent distributional differentiation was influenced by environmental variations; the dispersal of sp. II in southwestern Scandinavia was facilitated by a broader euryhalinity than that in sp. I and other stenohaline "glacial relief" crustaceans. The Irish populations may represent a distinct refugial stock within sp. II.