In our previous study, an antibiotic mixture treatment in f/2 agar medium containing KAS-antibiotics make orange pigmented Flavobacteriaceae bacteria strains GF1, which produce zeaxanthin, dominant in a Symbiodiniaceae culture. To confirm effects of the antibiotic mixture in bacteria community of Symbiodiniaceae cultures, we performed 16S rRNA amplicon sequencing of microalgal cultures before and after the antibiotics treatment. Paired-end DNA sequencing of the 16S rRNA V1/V2 region was performed on the Illumina MiSeq platform. The variable region V1/V2 of the 16S rRNA gene was amplified using 27Fmod-338R primers. Cladocopium sp. (NIES-4077) originally isolated from the bivalve Fragum sp. was provided by the NIES through the NBRP of the MEXT, Japan. Cladocopium goreaui (CCMP2466) originally isolated from the anemone Discosoma sanctithomae was obtained from the Bigelow Laboratory for Ocean Sciences (West Boothbay Harbor, ME, USA). Durusdinium sp. SGF was isolated from the coral Galaxea fascicularis.