Sampling of coral reef ecosystems in the Caribbean has been a challenge to resource managers for many reasons ranging from the lack of resources and communication, to unreported harvesting and jurisdictional boundaries. Because of these difficulties, the need exists to develop a program that does not rely on the infrastructure and public cooperation to estimate fish and habitat quality and abundance. Additionally, many of the reefs in the Gulf and Caribbean are ecologically and evolutionarily linked, requiring a quantitative, consistent sampling approach to make temporal and areal comparisons and provide understanding beyond the local level. Multiple fish and coral monitoring programs exist regionally, but all are limited in scope, scale, or not designed to answer the multi-scalar questions for basin-level problems. Over the past decade, NOAA Fisheries and National Ocean Service developed a suite of monitoring tools under the National Coral Reef Monitoring Program (NCRMP) to provide a simplified approach to long-term monitoring coral reefs at the ecosystem level to provide vital information on fish, coral, and habitats. Protocols exploit habitat-organism relationships that exist on coral reefs providing an iterative, stratified random sampling design that allows for optimal sample allocation with fewer samples. Among locations, organisms of interest may vary depending on the high-value species present or local interests, but functional groups remain similar, making cross-ecosystem comparisons possible. Here, we describe the history, methods, and future of the NCRMP as a tool to unify sampling across the Gulf and Caribbean to aid in ecosystem evaluation, fishery management, sanctuary efficacy, habitat conservation, and enhance uniformity of the Global Coral Reef Monitoring Network for reporting and product development.