Marine Protected Areas (MPAs) are promoted as an important marine ecosystem management tool. However, they are complex systems that, from a governance perspective, raise serious challenges with regard to their effectiveness. In this paper, drawing on recent contributions to the so-called “interactive governance theory,” the authors argue that marine and coastal governance is basically a relationship between two systems, a “governing system” and a “system-to-be-governed.” The former system is social: it is made up of institutions and steering mechanisms. The latter system is partly natural, partly social: it consists of an ecosystem, and the resources that this harbours, as well as a system of users and stakeholders who, among themselves, form political coalitions and institutions.