This data compilation includes benthic and fish survey data collected in St. Croix, St. John and St. Thomas, US Virgin Islands (USVI); La Parguera, Guanica, Jobos Bay, and Vieques, Puerto Rico; and Flower Garden Banks National Marine Sanctuary (FGBNMS) in the Gulf of Mexico. Data were collected on a biennial basis from 2001 through 2012 and in a consistent manner with established protocols by NOAA's NCCOS Biogeography Branch. In 2013, these long-term Caribbean and FGBNMS monitoring efforts merged with other monitoring programs funded by Coral Reef Conservation Program to form the National Coral Reef Monitoring Program (NCRMP), an ongoing program designed to monitor and assess changes in the composition of coral and reef fish communities.