A collaborative research effort between the NOAA’s National Centers for Coastal Ocean Science (NCCOS), Center for Coastal Monitoring and Assessment’s (CCMA) Biogeography Branch (BB) and the National Park Service South Florida and Caribbean Network (NPS-SFCN) has been inventorying and assessing reef fish populations in reef and reef-associated habitats in the northeast region of St. Croix from 2001-2011. The diver-based fish and benthic community survey methods were developed at the scale of the NPS MPAs (Buck Island in St. Croix and Coral Reef National Monument and National Park in St. John) and adjacent non-protected habitats. The methods were developed with the desire to expand to greater spatial scales, e.g., all of St. Croix or all of St. Thomas and St. John. Region-wide population metric estimates are required to effectively manage reef fisheries but are also imperative for spatial management and understanding ecosystem-level processes, such as measuring MPA efficacy. To date, very little information exists outside the northeast portion of St. Croix and this effort was designed to establish a baseline characterization for the whole island of St. Croix. This effort was also a logistical, as well as statistical primer, for the implementation of the National Coral Reef Monitoring Program (NCRMP) that will start in 2016. This program will implement standardized fish and benthic community survey across the USVI, Puerto Rico, Florida Keys and Flower Garden Banks National Marine Sanctuary (and a similar structure in the US Pacific) and serve as a broad scale monitoring tool for the foreseeable future. In May 2012, NOAA and NPS led a multiagency mission to conduct a comprehensive assessment of fish and benthic communities at depths between 1-100 feet (0.5-30 m) around the island of St. Croix. The mission included over 35 participants from NOAA-NCCOS, NOAA’s Southeast Fisheries Science Center (SEFSC), the National Park Service (NPS, South Florida/Caribbean Network - Miami, St. John, and St. Croix), U.S. Virgin Islands Department of Planning and Natural Resources (DPNR), The Nature Conservancy (TNC), the University of the Virgin Islands (UVI, St. Thomas campus and St. Croix campus), and the University of Miami. The survey design implements a stratified random approach built around metrics from pre-existing data from the northeast region and extrapolated to the whole island. Stratification comprises five hardbottom benthic habitats, two depth zones (less than and greater than 9.1m (30ft), and region (Table 1). There are seven regional strata including three marine protected areas (MPAs)-Buck Island Reef National Monument (BUIS) managed by the NPS; St. Croix East End Marine Park (STXEEMP) managed by the USVI DPNR; and, the Salt River Bay National Historic Park and Ecological Preserve (SARI) co-managed by NPS and USVI DNR (Figure 1). NOAA developed benthic habitat maps in 2001 where soft and hard bottom habitats were delineated from nearshore to depths near 30m (~100 ft).