In this study we investigated the microbial communities within the xenic diatom monocultures. Diatoms were isolated from four loggerhead sea turtles (from their carapace and skin) and grown in monocultures for several months prior to collecting biomass for amplicon sequencing of the V4 region of the 16S rRNA gene. These data are related to the study Filek et al. 2022 "More than just hitchhikers: a survey of bacterial communities associated with diatoms originating from sea turtles" FEMS Microbiology Ecology, fiac104, doi:10.1093/femsec/fiac104 and preprint Filek et al. 2022 "More than just hitchhikers: a survey of bacterial communities associated with diatoms originating from marine reptiles" bioRxiv 2022.04.19.488760 doi:10.1101/2022.04.19.488760