Most marine species in the Skagerrak have populations that are genetically distinct from populations in the surrounding North Sea, Kattegat, and Baltic Sea. A considerable number of these species also have multiple distinct populations within the Skagerrak, particularly along the coast and inside fjords. Overall, the Skagerrak is well connected with adjacent seas through passive dispersal of eggs and larvae and active migration of adults. The persistence of distinct local populations despite the large potential for connectivity calls for population-specific conservation and management of marine biodiversity in the Skagerrak. Management should therefore strive to be ecosystem-based, yet species- and population-specific to avoid neglecting or overexploiting vulnerable local populations.