Blue mussels, Mytilus edulis, Linnaeus 1758 from southern Barnegat Bay, New Jersey were examined to determine the make-up of the normal blue mussel microbiome. Sequencing of 16S ribosomal DNA amplicons from gill and intestinal content microbiomes using the Illumina® MiSeq platform yielded 1,276,161 paired end sequence reads from the gill libraries and 1,092,333 paired end sequence reads from the intestinal content libraries. General bioinformatic analyses were conducted with the open-source packages Qiime and Mothur. Phylotype assignments to the genus level were made using the commercial One Codex platform. This resulted in 1,697,852 gill and 988,436 intestinal content sequences being classified to genus. A majority of these (67.6% and 37.2% respectively) were assigned to a single operational taxonomic unit (Mytilus edulis Symbiont, MeS) that has homologies with other recently described Endozoicomonas pathogens and symbionts of marine invertebrates. MeS shares 98% identity with an uncultured bacterium from the gill tissue of an invasive indo-Pacific oyster and with HQE1 and HQE2 isolated from the sea squirt, Styela clava. Other than MeS, most of the detected bacterial species are known from marine sediments and seawater.