Rapid improvements in the technology used to assess microbial communities have led to an expansion of the breadth and scope of microbial ecology research over the past 20 y. The rapid increase in microbiome research, spurred by nextgeneration amplicon sequencing, has allowed researchers to characterize the microbial communities of organisms and environments which were previously poorly understood. Research on marine invertebrates is still developing, with the mechanisms that determine interactions between the host and their associated microbes largely unknown. Bivalves are of particular interest because of their crucial ecological and economic roles. With the anticipation of shifting environmental conditions, defining the natural variation and role of bivalve-associated microbes is vital to more complex research questions. The current knowledge of the spatial and temporal distributions of bivalve-associated microbes, microbial functional and genetic diversity, host-specific and tissue-specific interactions, and core microbial community composition is summarized here, as well as the beginning stages of understanding the role of microbiome in bivalve physiology and disease susceptibility.