Biodiversity loss is a global crisis that negatively impacts ecosystem functioning at both local and global scales. The UN CBD Kunming Montreal Biodiversity Framework specifically states maintenance of genetic biodiversity as equally important to species and ecosystem diversity. Failure to correctly identify genetic population structure and connectivity in the marine environment can result in the isolation and disappearance of vulnerable and threatened local populations, as well as the overharvesting of depleted fish stocks. Summarising current scientific knowledge on genetic population structure and connectivity in marine species inhabiting the Skagerrak Sea, we here provide information that can improve species- and ecosystem conservation, harvesting and marine spatial planning in the area.