Aquaculture is contributing to about 50 percent of global fish production and in most parts of the world fish capture production has stagnated for over a decade because maximum sustainable yields have been reached. Therefore the increasing demand for fish has to be met by increasing fish production by aquaculture. This has been a challenge because disease outbreaks have been causing serious losses in both finish as well as shellfish aquaculture. Detection of residues, in some countries, of certain banned antibiotics in aquaculture products has led to consumer concerns about the safery of these products. There is also growing concern about the emergence and spread of bacteria resistant to antimicrobial agents and transfer of resistance determinants to human pathogens that may be associated with the aquatic environment. In this context, there is a need to look for alternatives to antimicrobial agents for health management in aquaculture. Most often, disease problems in aquaculture are because of a shift in the delicate balance between the host, the pathogen and the environment. Therefore, disease problems can be significantly reduced by adopting good management practices. In the aquaculture of salmonids, the use of antimicrobials could be minimised substantially by vaccinating fish against some of the common bacterial and viral diseases. However, currently, no vaccines are available for parasitic diseases. Further, global aquaculture is dominated by Asian cyprinids and currently, there are no commercial vaccines available for these species. Crustaceans have a poorly developed immune system and there are no commercial vaccines for this sector of aquaculture. However, the innate immune response of fish and crustaceans can be stimulated by certain microbial molecules like glucans that can act as immunostimulants. Currently, immunostimulants are widely used for health management both in finfish as well as crustacean aquaculture.