Aquaculture is the fastest growing food-producing sector, providing an acceptable supplement to and substitute for wild fish and plants. Increased production intensification, particularly in high-value species, involves substantial stress, which, as in other captive livestock species, has resulted in outbreaks of major diseases and related mortalities. Widespread use of antibiotics has led to the development of antibiotic-resistant bacteria and the accumulation of antibiotics in the environment and the flesh of fish. Thus, recently effort has been dedicated to vaccine development. Vaccination in fish is complicated by their aquatic environment. Individual injections are labor-intensive and stressful, since fish have to be removed from the water and anaesthetized. Some vaccines offer a limited duration of protection, and thus booster applications are required. In salmonid species, many commercial vaccines use oil-based adjuvants, resulting in a greatly improved duration of protection. However, oil-based adjuvants have been related to significant growth depression, internal adhesions and injection site melanization, resulting in carcass downgrading. Oral administration to aquatic species is by far the most appealing method of vaccine delivery: there is no handling of the fish, which reduces stress; and administration is easy and suitable for mass immunization. However, few oral vaccines have been commercialized, due in part to the increased quantity of antigen required to provoke an immune response, and the lack of an adequate duration of protection. For effective oral delivery, protective antigens must avoid digestive hydrolysis and be taken up in the hindgut in order to induce an effective protective immune response. Antigen encapsulation technologies have been used to protect antigen; however, such strategies can be expensive and are not always effective. Alternative approaches, currently under development, are discussed.