Stony corals associate with a broad array of microbial partners that can influence the health, performance and survival of tropical reef ecosystems. While current research is largely focused on the nutritional benefit of microbial Eukaryotes (i.e., Symbiodinium sp.), less is known about the role of bacteria and Archaea partners in this system. This protocol describes the methods used to extract coral-holobiont gDNA and generate 16S amplicon libraries in preparation for MiSeq Illumina sequencing.