The present study uses two differential extraction methods (sequential, maceration) to identify bioactive compounds present in two seaweeds Gracilaria folifera and Sargassum longifolium. Five different solvents namely Petroleum ether, Dichloromethane, Chloroform, ethanol and water were used. The bioactive compounds present in the extracts showed antioxidant and antibacterial activities against Aeromonas salmonicida. Ethanol and aqueous extracts of these seaweeds were found to have better antibacterial activity against bacterial diseases in fish when compared to the other extracts. Toxicological and in vivo pathogenicity studies were performed with the highest concentration of 250. mg/l of extracts. The compounds identified by GC-MS which were found to have antibacterial activity were prepared in the form of a colloidal suspension for oral treatment. The use of algal extracts in aquaculture disease management is a cost effective and eco-friendly approach. These extracts could be used as prophylactics. © 2015 Elsevier B.V.