The European green crab, Carcinus maenas, has a native distribution that extends from Norway to Mauritania. It has attracted attention because of its recent invasions of Australia, Tasmania, South Africa, Japan and both coasts of North America. To examine the population structure of this global invader in its native range, we analysed a 502-base-pair fragment of the mitochondrial cytochrome c oxidase I (COI) gene from 217 crabs collected in the North Atlantic and 13 specimens from the Mediterranean. A clear genetic break (11% sequence divergence) occurs between the Mediterranean and Atlantic, supporting the species-level status of these two forms. Populations in the Faeroe Islands and Iceland were genetically distinct from continental populations (FST = 0.264–0.678), with Iceland represented by a single lineage also found in the Faeroes. This break is consistent with a deep-water barrier to dispersal in green crabs. Although there are relatively high levels of gene flow along the Atlantic coast of Europe, slight population structure was found between the central North Sea and populations to the south. Analysis of variance, multidimensional scaling, and the distribution of private haplotypes support this break, located between Bremerhaven, Germany, and Hoek van Holland. Similar biogeographical and genetic associations for other species, such as benthic algae and freshwater eels, suggest that the marine fauna of Europe may be generally subdivided into the areas of Mediterranean, western Europe and northern Europe.