Marxan is the most widely used software in conservation planning around the world providing spatially explicit decision support for a range of conservation planning problems. This systematic conservation approach provides objective, transparent and repeatable results that allow spatial visualizations of areas being considered conservation and facilitates the negotiation process with stakeholders. This case study describes the process followed to identify major ecological important areas and define a network of marine priorities areas in order to minimize the main threats affecting the new Puerto Rico Marine Corridor of the Northeast. Our conservation objectives included the representation of endangered and vulnerable species and habitats. Data collected in the area from different regional and federal agencies and academic institutions was incorporated and analyzed following expert-defined criteria. In order to achieve feasible and efficient conservation outcomes, a detailed analysis of multiple threats and stressors was also incorporated. Scenarios were mapped showing networks of priority areas and biodiversity hotspots based on a range of different conservation targets. These scenarios will guide resource managers tasked with developing an integrated management plan for the Marine Corridor of The Northeast.