Globally, conflicts between marine nature conservation and fishery interests are common and increasing, and there is often a glaring lack of dialogue between stakeholders representing these two interests. There is a need for a stronger and enforced coordination between fishing and conservation authorities when establishing marine protected areas for conservation purposes. We propose that an appropriate instrument for such coordination is a broad ecosystem-based marine spatial planning procedure, representing neither nature conservation nor fishery. Strategic environmental assessment for plans and programmes and environmental impact assessment for projects are commonly used tools for assessing the environmental impacts of different human activities, but are seldom used for evaluating the environmental effects of capture fisheries. The diversity of fisheries and the drastic effects of some fisheries on the environment are strong arguments for introducing these procedures as valuable supplements to existing fisheries assessment and management tools and able to provide relevant environmental information for an overall marine spatial planning process. Marine protected areas for nature conservation and for protection of fisheries have different objectives. Therefore, the legal procedure when establishing marine protected areas should depend on whether they are established for nature conservation purposes or as a fisheries resource management tool. Fishing in a marine protected area for conservation purpose should be regulated according to conservation law. Also, we argue that marine protected areas for conservation purposes, in the highest protection category, should primarily be established as fully protected marine national parks and marine reserves.