In order to achieve the Aichi Target 11 of the Convention on Biological Diversity, attentions are being focused on the role of local ecosystem service users. Marine protected areas (MPAs) in Japan is defined by the Marine Biodiversity Conservation Strategy of 2011, and marine areas managed by local fishers for sustainable resource uses are included in the list of Japanese MPAs. MPAs set by local fishers are generally flexible and can be compatible to the locally specific objectives or issues. In addition, such MPAs can partly contribute to the ecosystem structure and biodiversity conservation. Also, statistics and traditional knowledge of local fishers can be the base of effective ecosystem monitoring system. However, they are not enough mainly for the following two reasons. First of all, the spatial scale of the local fisheries management is smaller than the biodiversity conservation. Secondly, there are many ecosystem services provided from ecosystems, and therefore, many users (stakeholders) other than fishers, but each use is managed by vertically segmented sectoral laws. We need the integrated ecosystem conservation policy framework including all the sectors relating to marine ecosystem service uses.