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Changes in marine environments, including pH changes, have been correlated to alterations in the physiology and disease susceptibility of cultured organisms at the early stages of development. In this study, high-throughput sequencing of the V3-V4 region of the 16S rRNA gene was performed to evaluate the bacterial biodiversity of Crassostrea gigas pediveliger larvae and spat under acidic stress compared to that of larvae at normal pH value. The evaluation was performed in an experimental system with continuous water flow and pH manipulation by CO2 bubbling to simulate acidification (pH 7.38 +/- 0.039), using the current ocean pH conditions (pH 8.116 +/- 0.023) as a reference. The results indicated that the bacterial communities associated with both pediveliger larvae and spat were modified in response to acidic conditions. The families Rhodobacteraceae and Campylobacteraceae were the most affected by the change in pH, with increases in Vibrionaceae in pediveliger larvae and Planctomycetaceae and Phyllobacteriaceae in spat detected. The results of this study demonstrate that the bacterial communities associated with C. gigas pediveliger larvae and spat are responsive to changes in ocean acidification.