Aquaculture is one of the principal sources to increase the world's fish production. Outbreak of diseases is a major problem in aquaculture. Chemotherapeutic approaches have been used for the treatment and prevention of disease outbreaks. The use of various chemicals has harmful effects on the environment and human health. The prolonged use of antibiotics causes antibiotic resistance. Natural products such as medicinal plants, marine algae, herbs and their extracted compounds are being studied for disease management in fishes and prawns. In this review, the use of seaweeds and their importance in aquaculture health and disease management to control the bacterial infections against the pathogenic bacteria which affect freshwater fishes is explained. Application can either be by a single compound or a combination of two different compounds or as feed additives. Administering the compounds obtained from the extracts in the form of encapsulated beads was found to be more effective. Statement of relevance Seaweeds have good antioxidant capacity and act as a natural medicine. Bacterial fish pathogens affect the health of aquatic organisms. The bioactive compounds from sea weed extracts showed good antibacterial activity. They can be used for treating bacterial infection in aquaculture and as prophylactis. This kind of prophylactic treatment can be used as an alternative to synthetic since they cause resistance. © 2016 Elsevier B.V.