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In the present study, we compared mucus and gut-associated prokaryotic communities from seven nudibranch species with sediment and seawater from Thai coral reefs using high-throughput 16S rRNA gene sequencing. The nudibranch species were identified as Doriprismatica atromarginata (family Chromodorididae), Jorunna funebris (family Discodorididae), Phyllidiella nigra, Phyllidiella pustulosa, Phyllidia carlsonhoffi, Phyllidia elegans, and Phyllidia picta (all family Phyllidiidae). The most abundant bacterial phyla in the dataset were Proteobacteria, Tenericutes, Chloroflexi, Thaumarchaeota, and Cyanobacteria. Mucus and gut-associated communities differed from one another and from sediment and seawater communities. Host phylogeny was, furthermore, a significant predictor of differences in mucus and gut-associated prokaryotic community composition. With respect to higher taxon abundance, the order …