Monogeneans are the most common external parasites of fishes, sharks, amphibians and crustaceans living in fresh and saltwater. The simple life cycle of these monoxenous parasites allow them to grow rapidly in aquatic habitats such as aqua farms and aquariums, causing extensive damage to the aquaculture industry by harming their host and contaminating other aquatic organisms in the environment. Several studies have been done on parasitic infections of aquatic animals, especially monogeneans, as well as their immune system, and also the interactions between the parasite and the host, all of which confirm the prevalence of these infections among aquatic animals. Though many efforts have been done to cure the aquatic infections, these diseases have been remained one of the main challenges in aquaculture. Chemical therapies are effective, but still have their own problems regarding the aquatic safety such as drug resistance and environmental considerations due to the releasing of chemical and antimicrobial drugs. In recent decades, efforts have been made to develop effective vaccines to protect aquatic species, but vaccination against parasitic infections has remained an unresolved issue due to the specific living conditions of parasites and resistance to the immune system. Studies on aquatic nutrition have also shown that fortifying of the aquatic feeds can be effective in strengthening the immune system and increasing aquatic resistance.