The health of marine bivalve larvae is greatly affected by bacteria in the environment particularly when reared in marine hatcheries. This is generally because high stocking densities resulting in high organic loads of both food and faeces, can support increased bacterial growth and biomass levels. Increased bacterial load can lead to larval disease referred to as bacillary necrosis (BN) leading in turn to rapid larval mortality and loss of production. Despite more than 50 years since the first detailed description of BN, westill do not fully understand its causes and mechanisms. Through the manipulation of a model larval culture of the Australian blue mussels (Mytilus galloprovincialis), we determined that BN is linked with rapid and systematic changes in the bacterial community.