The Skagerrak is a productive miniature deep sea with diverse habitat and nature types harbouring genetically distinct marine populations. Nature protection in the Skagerrak consists of marine protected areas (MPAs) ratified under the OSPAR agreement (EU and non-EU members), the Natura 2000 network of MPAs (EU member states) and national parks. Preliminary analyses suggest that marine protection in Skagerrak is weak overall, especially considering areas with regulation of bottom-contacting fisheries. Further, protected areas in Skagerrak are largely restricted to shallow coastal areas, meaning that 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.