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The loss of coral habitats and associated biodiversity have direct effects both on the physical dynamics of the coast and on natural resources, threatening the survival of local populations. Conservative actions, such as the creation of new Marine Protected Areas, are urgent measures needed to face climate change. Managers need fast and simple methods to evaluate marine habitats for planning conservation areas. Here, we present the application of an Ecological Quality Index (EQI), developed for regional-scale habitat maps of the Atlas of the Marine Coastal Habitats of the Kingdom of Tonga, by processing Copernicus Sentinel-2 imagery. Both the habitat mapping classification and the EQI application were focused on the importance of coral reef, seagrass and mangrove habitats, both as natural defense and sustenance for the local populations. Twelve main Pacific reef habitats were evaluated through a three-level EQI score assigned to six parameters: nursery ground, connectivity, species reservoir, fish attraction, biodiversity and primary production. The EQI was integrated into a developed georeferenced database associated to the QGIS software providing the ability to identify on the maps the area of interest and the associated habitats, and to quantify their ecological relevance. The EQI is proposed as a tool that can offer to stakeholders and environmental managers a simple and direct indicator of the value of the marine coastal environment. The index may be handled for management purposes of vast areas with remote and uninhabited islands. [ABSTRACT FROM AUTHOR]