biostudies-literatureUnknown40Cram JAWe present oyster larval microbiota from two feeding studies, in which wild type and low-salinity tolerant lines were either fed or starved. In one study, all larvae unexpectedly died, which was concurrent with an event in which all larvae in an adjoining oyster hatchery also died. In the other study, no crash occurred in either the study or hatchery. In both cases, larvae were collected and stored frozen, and microbial and host DNA was isolated by phenol-chloroform extraction. Both host 18 s rRNA genes and microbial 16 and 18 s rRNA genes were sequenced using universal primers. We present raw sequences, the pipeline that was used to quantify amplicon sequence variants, and our analysis pipeline that we used to describe how the overall microbial community varied between projects (crashed aData in brief107755https://www.ebi.ac.uk/biostudies/studies/S-EPMC8732746biostudies-literatureMicrobiota of <i>Crassostrea virginica</i> larvae during a hatchery crash and under normal production: Amplicon sequence data.PMC8732746Hollins AMcFarland KGray MWCram JAfalseMicrobiota of <i>Crassostrea virginica</i> larvae during a hatchery crash and under normal production: Amplicon sequence data.We present oyster larval microbiota from two feeding studies, in which wild type and low-salinity tolerant lines were either fed or starved. In one study, all larvae unexpectedly died, which was concurrent with an event in which all larvae in an adjoining oyster hatchery also died. In the other study, no crash occurred in either the study or hatchery. In both cases, larvae were collected and stored frozen, and microbial and host DNA was isolated by phenol-chloroform extraction. Both host 18 s rRNA genes and microbial 16 and 18 s rRNA genes were sequenced using universal primers. We present raw sequences, the pipeline that was used to quantify amplicon sequence variants, and our analysis pipeline that we used to describe how the overall microbial community varied between projects (crashed a2022-01-01T00:00:00Z2022 Feb2025-04-03T22:46:25.959Z2022-02-11T16:19:42.662ZS-EPMC87327463502439410.1016/j.dib.2021.107755