This dataset is an important part of the project, namely Ecogenomics of viruses in two coral reefs in Vietnam: Phu Quoc and Con Dao Islands. In this project, we collected some microorganisms for the investigation of the microbial diversity and ecology associated with coral reefs in Phu Quoc and Con Dao Islands. This dataset included raw reads sequences of 16S rRNA genes, which were collected from healthy and grazed coral species, seawater and sediment.