Most 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. Highly mobile fish species, such as cod, herring and bluefin tuna, have multiple distinct populations that temporarily coexist in the Skagerrak during specific parts of the year, or during certain parts of their life cycle. 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, while maintaining an overall ecosystem approach, needs to be species- and population-specific to avoid neglecting or overexploiting vulnerable local populations.