The Caribbean is a mega-diverse and bio-geographically important region that consists of the Caribbean Sea, its islands, and surrounding coastlines. Among the billions of aquatic species inhabiting this region, the mega-vertebrates stand out for their social, economic and ecologic relevance. However, the Caribbean has been threatened by climate change, poverty, pollution, environmental degradation and intense growth of the tourism industry, affecting megafauna species directly and indirectly. Population monitoring plays a critical role in an informed conservation process and helps guide management decisions at several scales. The aim of the present review was to critically examine the methods employed for monitoring marine megafauna in the Caribbean, so as to create a framework for future monitoring efforts. In total, 235 documents describing protocols for the monitoring of sirenians, cetaceans, elasmobranchs, sea turtles and crocodilians in the Caribbean region, were reviewed. The methods included community-based monitoring (interviews, citizen science and fisheries monitoring), aerial surveys (by manned and unmanned aerial vehicles), boat-based surveys (including manta tow, and side-scan sonars), land-based surveys, acoustic monitoring, underwater surveys, baited remote underwater video, mark–recapture, photo-identification and telemetry. Monitoring efforts invested on aquatic megafauna in the Caribbean have been highly different, with some species and/or groups being prioritised over others. The present critical review provides a country-based overview of the current and emerging methods for monitoring marine megafauna and a critical evaluation of their known advantages, disadvantages and biases.