Mussels along with clams and oyster represent the most important worldwide mollusk production. Among mussels, Mytilus chilensis and Mytilus galloprovincialis are the most important species, exceeding 300,000 tons, but other species like Mytilus edulis and Mytilus californianus have significant production. In this chapter, we focus on the relevance of mussel microbiota for aquaculture and, specifically, for human health. In some sections, due to the limited documentation available, information has been expanded to studies in other mollusks, such as oysters and clams, as a significant reference for future studies on mussels. Anyway, information on mollusk microbiota lags behind other aquaculture species, particularly fish, and this limitation is discussed in this chapter. Then, the demand for further work is highlighted considering the benefits of microbiota control for mollusk production and health.