Aquaculture of the eastern oyster (Crassostrea virginica ) is a rapidly expanding and economically important industry. Probiotics are an increasingly popular approach for prevention of diseases in aquaculture . The marine bacterium Phaeobacter inhibens S4 (S4) protects larval eastern oysters against challe nge with the bacterial pathogen Vibrio coralliilyticus RE22. A liquid formulation of probiont S4 has been developed for commercial use in shellfish hatcheries. The goal of this research is to determine the effect of the S4 formulation on the microbial communities of larvae raised in the hatchery, in order to understand how the larval bacterial community may change due to probiotic treatment and how this microbial community may contribute to larval health, growth, and development. Probiont S4 (104 CFU/ml) was delivered daily to C. virginica larvae culture tanks from day 1 to day 8 post spawning during eight different trials in four different hatcheries, and structure and diversity of bacterial communities in larval oysters was analyzed as compared to control (no probiont ) tanks using 16S rRNA amplicon sequencing. The effect of the probiont S4 formulation on the larval bacterial communities differed by hatchery, season, and type of water treatment (ultraviolet (UV) irradiation/nonUV treatment). The S 4 probiont altered the bacterial communities in the larvae and had a targeted effect on the abundance of specific bacteria taxa, including Alteromonadales , Rhodobacterales , Oceanospirillales , Bacillales and Vibrionales . This study contributes to better und erstanding of the mechanisms of action of the probiont S4 liquid formulation and aids in optimizing its use and benefits for commercial culture of eastern oyster larvae and preventing undesirable side-effects. Further analyses will focus on potential relationships between bacterial community structure and environmental parameters collected during the hatchery trial.