A prebiotic is a non-digestible food ingredient that beneficially affects the host by selectively stimulating the growth and/or the activity of one or a limited number of bacteria in the colon. Despite the potential benefits to health and performance as noted in various terrestrial animals, the use of prebiotics in the farming of fish and shellfish has been less investigated. The studies of prebiotics in fish and shellfish have investigated the following parameters: effect on growth, feed conversion, gut microbiota, cell damage/morphology, resistance against pathogenic bacteria and innate immune parameters such as alternative complement activity (ACH50), lysozyme activity, natural haemagglutination activity, respiratory burst, superoxide dismutase activity and phagocytic activity. This review discusses the results from these studies and the methods used. If the use of prebiotics leads to health responses becoming more clearly manifested in fish and shellfish, then prebiotics might have the potential to increase the efficiency and sustainability of aquaculture production. However, large gaps of knowledge exist. To fully conclude on the effects of adding prebiotics in fish diets, more research efforts are needed to provide the aquaculture industry, the scientific community, the regulatory bodies and the general public with the necessary information and tools.