We sequenced 16S rRNA gene amplicon surveys of 28 samples of deep-sea corals Acanthogorgia aspera, Acanthogorgia spissa, Desmophyllum dianthus, and Lophelia pertusa (Desmophyllum pertusum), as well as an extraction blank for the Qiagen PowerBiofilm kit used for DNA extraction. The samples were collected during four research cruises from various locations in the Gulf of Mexico and the Atlantic Ocean off the east coast of the United States in deep-sea coral ecosystems from 2013 to 2019 for microbial analysis. Samples were preserved in RNAlater, and sequenced using Illumina MiSeq.