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Intensification of aquaculture has led to frequent occurrence of disease outbreaks. To deal with this issue antibiotics are a widely-preferred control strategy, but one that poses risks to the environment and humans, if used indiscriminately. In pursuit of an alternative, probiotics have emerged recently among viable alternatives for health management in aquaculture. The prophylactic use of probiotics in farmed shellfish species, i.e., shrimp, prawn, crab, crayfish, oyster and abalone, has been demonstrated to enhance production, promote the host internal microbiota, resulting in reduced incidence of bacterial, parasitic and even viral (e.g., White Spot Syndrome Virus/WSSV, Yellowhead disease/YHD) diseases. Probiotics can be administered either as feed supplements or directly into rearing water, the former being generally more effective. Although precise modes of action are unknown, probiotics can deliver some measure of sustainability to shellfish aquaculture in multiple ways, including contributions to pathogen exclusion, better growth, survival and feed utilization, and immune modulation. Antiviral mechanisms of probiotics are not well documented, but certain protobionts such as Bacillus and Lactobacillus have been effective in developing disease resistance and in reducing the prevalence of WSSV and YHD in a number of studies. This review discusses recent advances on the role of probiotics in shellfish aquaculture, emphasizing their prophylactic activity against viral diseases.