The Antillean manatee (Trichechus manatus manatus), a subspecies of the West Indian manatee, is listed as endangered by the US Department of Interior. In accordance with its listing, the U.S. Fish and Wildlife Service’s Caribbean Field Office (USFWS) is mandated to create one or more Manatee Protection Areas (MPAs) for Puerto Rico. Designation of these areas must comply with the legal definition of an MPA’s purpose: to prevent or reduce take of manatees (CFR 50: 44 FR 60964, Oct. 22, 1979). To meet this goal, we pursued two objectives: 1) identify areas which include the specific ecological attributes necessary to support manatee populations, and 2) identify areas where take can be reduced through approved MPA regulatory frameworks. We achieved these objectives through literature review, expert elicitation, and geospatial modeling. This report delivers to USFWS a set of nine potential MPA regions. These regions represent the spatial realization of experts’ hypotheses regarding manatee requirements and threats, and the potential to implement MPA strategies (e.g. watercraft access, speed regulations, signage and boater education). The nine regions are compared based on a number of factors, including their potential to reduce take, quality of the habitat encompassed, and total area. These maps and statistics serve as suitable starting points to select one or more MPA sites, but we recommend that the mapped attributes and threats (i.e., boating activity) of MPAs be ground-truthed to visually confirm the local presence of resources, threats, and manatees before any area is selected. Once established, the effectiveness of MPAs can be monitored and updated through processes of adaptive monitoring and management. Aerial surveys, radio tracking studies, and public surveys are all valuable tools to assess the success of an MPA. Establishing MPAs is a management action that, integrated within the species Recovery Plan, should enhance the conservation of manatees.