Cuba’s expansive coral reefs and mangrove habitats provide a variety of ecosystem services to coastal communities including nursery grounds for fisheries, shoreline stability, and storm and flood protection. While Cuba’s coastal habitats are some of the most preserved in the Caribbean, they are under increasing threat of degradation from the impacts of climate change, increased tourism, and coastal development. With the goal of sustainable development, Cubans need to assess the storm and flood protection benefits these coastal habitats provide, and integrate this information into future expansion and management plans within the National Protected Areas System (SNAP). Using the open source software, Integrated Valuation on Ecosystem Services and Tradeoffs (InVEST), a national-scale coastal vulnerability model was developed to provide quantitative estimates of coastal exposure and the protective role of coastal habitats during storm events. This model integrates storm information with bathymetry and coastline geomorphology, coupled with coastal habitat data to estimate the influence of these habitats in reducing vulnerability to storms and flooding. By combining these results with human population data, the model identifies where coastal communities are most vulnerable to wave energy and storm surge, and where coral reefs and mangroves provide the most protection by reducing impacts to these communities. We classify these regions as areas of conservation priority. We observed that fifty percent of the areas identified as areas of conservation priority lack any form of environmental protection. We recommend including these key habitats within the National System of Protected Areas. This will permit decision makers to more effectively concentrate restoration and conservation efforts in areas where people and natural resources will experience greater benefit from valuable ecological services.