Since production from capture fisheries cannot meet the demands of exports, aquaculture has subsequently played a major role in securing the raw materials for the world's food industries. Aquaculture has rapidly developed from extensive systems to semi-intensive, intensive and super-intensive systems. This has introduced the use of chemicals and drugs into the systems, which cause residual problems in the products. In the developed world, food safety has become a major issue of concern. The world market now demands healthy aquaculture products from farm to table. To achieve these requirements and to keep their markets, countries involved in aquaculture have implemented control measures such as farm licensing, code of conduct for sustainable aquaculture, hazard analysis and critical control point (HACCP) and good aquaculture practice. However, infectious diseases in aquaculture are of major concern to the industry and are typically controlled by eradication of the pathogen, treatment with antibiotic or chemotherapeutics, and/or by preventative measures such as the use of probiotics or vaccines. To limit the use of chemicals and antibiotics, good farm management is highly recommended. In terms of treatment, chemicals and antibiotics should be evaluated to establish recommended doses and withdrawal periods, otherwise alternative treatments should be developed. Environmentally-friendly probiotics have been introduced to aquaculture practice in the last decade to replace pathogenic bacteria with beneficial bacteria transient in the gut. Micro-organisms have also been prepared for the purpose of biocontrol and bioremediation. The application of probiotic, biocontrol and bioremediation seem promising; however considerable efforts of further research in terms of food and environmental safety are needed. Vaccination has proved highly effective in controlling diseases in the salmon industry mainly in Europe, America and Japan. In other Asian countries, this practice seem to be slower to develop due to differences in the aquaculture systems used and the economic value of the fish species farmed. Because shrimp farming is a large industry in this region, much effort has been put into developing a vaccine for viral diseases of shrimp. The efficacy of those vaccines remains inconclusive. Immunostimulants are another option developed for use in the shrimp industry in the region; however their efficacy also remains unclear.