Aquaculture is one of the fastest growing sector of food production in the world. Despite the encouraging trends, several constraints have had a negative impact on the growth of aquaculture. Diseases are the primary limiting factor in large scale production facilities, where aquatic animals are exposed to stressful conditions. Bacterial diseases are responsible for heavy mortality in both wild and cultured fish and result in serious economic lossess. Prevention and control of diseases have led during recent decades to a substantial increase in the use of veterinary medicines. However, the utility of anti-microbial agents as a preventive measure has been questioned, given the extensive documentation on the development and spread of antimicrobial resistance genes among bacteria. Several mechanisms can be responsible for the acquirement of antibiotic resistances, the main common of which are chromosomal mutation or acquisition of plasmids. Chromosomal mutations cannot be transferred to other bacteria but plasmids can transfer resistance rapidly. Several bacterial pathogens can develop plasmid-mediated resistances: plasmids carrying genes for resistance to antibiotics have been found in marine Vibrio species and they could be laterally exchanged. The concept of biological disease control using probiotics has received widespread attention during the last decade. When looking at probiotics intended for an aquatic usage, it is important to take into account the complex relationship that an aquatic organism has with its direct environment, compared to terrestrial animals. Gram-negative facultative anaerobic bacteria are dominant in fish and shellfish digestive tract, but the intestinal microbiota of aquatic animals may change very rapidly with the ingestion of microorganisms coming from water and food. This is probably the reason why a large number of probiotics developed in aquaculture are bacteria directly originating from the aquatic environment. However, more ‘traditional’ bacterial or yeast species marketed for animal nutrition (Lactobacillus spp., Pediococcus spp., Bacillus spp., and S. cerevisiae) are also used. They can target fish eggs and larvae, fish juveniles and adults, crustaceans, bivalve molluscs and also live food such as rotifers, artemia, or unicellular algae (Kesarcodi-Watson et al., 2008). Growth-promoting effects, through better feed utilisation and digestion, as well as biological control of pathogen colonisation are the most important expected benefits of probiotic applications. Disease outbreaks caused by Vibrio spp. or Aeromonas spp. have been recognised as the most significant constraint on aquaculture production, particularly in the shrimp subsector, where vibriosis is currently one of the main diseases identified. Whereas in vitro, antagonism to pathogens has been clearly demonstrated for a wide range of probiotic strains, in vivo evidence of efficacy is still very scarce. Most probiotics proposed as biological control agents in aquaculture belong to the lactic acid bacteria (Lactobacillus spp. and Carnobacterium spp.), to the genus Vibrio (V. alginolyticus), to the genus Bacillus, or to the genus Pseudomonas, although other genera or species have also been mentioned (Aeromonas and Flavobacterium). Few multinational pharmaceutical companies have introduced commercial preparations into the market as probiotics feed/food supplement in various commercial names as Aqualact, Spilac, Protexin (Verschuere et al., 2000). This chapter will give some examples on how probiotics can be applied to reduce the incidence of diseases usually affecting aquatic animals, including fish, crustaceans and mollusks. Moreover, a brief consideration on the recent approach of prebiotic administration will also be provided.