Value of the data •These HTS datasets would help expand our knowledge of the source, distribution, selection, and nutritional benefit of the gut microbial communities in diverse species of marine echinoderms, and other marine invertebrates at various trophic levels. •The metagenome data provide for the first time an insight into the modulation of gut microbiota of laboratory aquaculture sea urchins fed with a standard formulated reference diet at the highest possible taxonomic coverage. •Access to the raw files of these HTS data permits researchers to apply their own bioinformatics analyses, based on their exploratory goals.