Benthic survey data provided in this data set were collected around Puerto Rico as part of NOAA National Centers for Coastal Ocean Science (NCCOS)-led missions in collaboration with various partners. These partners include the University of Puerto Rico, HJR Reefscaping, Ecoelectrica, Puerto Rico Department of Natural and Environmental Resources (Departamento de Recursos Naturales y Ambientales), the University of the Virgin Islands and the U.S. Department of Fish and Wildlife. This benthic data collection for the ongoing National Coral Reef Monitoring Program (NCRMP) consists of two survey types: the Line Point-Intercept (LPI) method and the Coral Demographic method. The LPI method provides a measure of percent cover of biotic and abiotic components of the benthos in a stratified random sampling design in hardbottom and coral reef habitats. LPI surveys are concurrent with and along the same transect as fish surveys. The coral demographics protocol provides more detailed and species-specific insight (‘signal magnitude’) for coral populations than is provided by percent cover.