In Puerto Rico, the environmental legislation for establishing marine protected areas (MPAs) is complex due to its current political position with the United States (US) as not only local but also federal US laws affect designations. Currently, of the 37 MPAs recognized and investigated in this work, the vast majority (73%) are Natural Reserves, followed by Commonwealth Forests (13.5%). Most MPAs in Puerto Rico were implemented using a top-down approach (i.e., government) which follows US federal guidelines for protecting endangered species, critical habitats, and natural and cultural resources. The development of management plans for MPAs on the island is increasingly adopting a public participatory process. However, this latter process is new for the government of Puerto Rico that has not incorporated a policy based on an Integrated Coastal Management.