The Skagerrak is a productive miniature deep sea with diverse habitat and nature types harbouring distinct marine populations. Marine protection in Skagerrak is weak overall, especially considering areas with regulation of bottom-contacting fisheries. Marine protected areas in Skagerrak (MPAs) are largely restricted to shallow coastal areas, meaning that vulnerable and ecologically important deep-water habitat types are poorly protected. The deepest parts of the Skagerrak are situated in the Norwegian Trench, which is home to vulnerable marine ecosystems, and constitute the most important carbon sink in the greater North Sea region. Establishment of a coherent network of MPAs in the Skagerrak will require international coordination, where marine spatial planning should consider the benefits of protection to biodiversity, fisheries and climate change adaptation and mitigation.