A total of 205 COI sequences and 310 cyt b sequences of the threespine stickleback (Gasterosteus aculeatus) from basins of all seas throughout the vast range of this species were analyzed. Median networks of haplotypes constructed in this study, combined with the results of reconstruction of paleogeographic conditions, led to the conclusion that the threespine stickleback emerged as a species in the Pacific Ocean basin and spread to Europe from the south, populating the system of water bodies that existed in the Oligocene. The main water body was the Paratethys Ocean (Sea), which existed 5–34 Mya. In the area of the modern North Sea, stickleback populations, part of which later migrated to the eastern and western coasts of North America, gave rise to the group of haplotypes that has the widest distribution in northern Europe. The stickleback populations belonging to the lineage that dispersed along the Arctic and western coasts of North America displaced the carriers of the haplotypes of the ancient phylogenetic lineage that inhabited the Pacific coast. The ancestors of G. wheatlandi dispersed from the Pacific to the Atlantic Ocean via the Arctic to meet G. aculeatus, which circled the globe from east to west.