In oligotrophic oceans, microbial communities sustain productivity in coral reef ecosystems. As the health and distribution of coral reefs decline worldwide, characterizations of the microbial compositions and metabolisms of coral reef biomes and surrounding seawater improve our understanding of these oases of nutrient cycling and species diversity. Seawater was collected from reefs at Jardines de la Reina (JR), Cuba, a reef system that is relatively sheltered from anthropogenic activity due to distance from shore and government protection and enforcement of no-take fishing regulations. The microbial community was examined through sequencing the bacterial and archaeal 16S rRNA gene.