The worldwide decline of coral reefs necessitates the development of strategies aimed at controlling coral disease. As a result, various biological approaches are being considered as tools for coral disease management. For example, phage therapy has been shown to be effective in removing pathogens under laboratory conditions, showing promise for the treatment of specific pathogens; in addition, mutualistic bacteria compete with pathogens and produce antibiotics, properties that are both known to be important for biological control. Here we evaluate the probiotic potential of native mutualistic bacteria as a means of controlling coral diseases caused by opportunistic pathogens or their consortia. Monitoring native coral-associated microbiota for functions associated with resistance to pathogens could also serve as an additional indicator of reef health.