These are amplicon sequence data of 16S and 18S rRNA genes (515FY-926R primers) of oyster larval microbiota. Host 18S genes are included in these data, and make up the bulk of the sequences. Larvae were collected from three or more time-points from 15 broods at the Horn Point Laboratory Oyster Hatchery. 9 broods experienced die-off events, or "crashes" in which fewer than 1 million larvae survived to the pediveliger stage, while the others did not crash and had more than 1 million survivors.