Sea weeds are valuable natural assets in aquaculture due to the presence of various bioactive active metabolites in them. Successful fish production and maintenance of disease free culturing systems in aquaculture with environment friendly practices is often affected by various environmental factors. Disease causing pathogens is one of the major factors. These can be controlled by the emerging technologies such as biopolymer based drug delivery systems, feed encapsulations processes and immersions of active ingredients which can possibly facilitate sustainable production by enhancing growth and immune responses in aquaculture animals. The focus of our study is on the identification of antibacterial and antioxidant compounds from two brown seaweeds, Gracilaria foliifera and Sargassum longifolium which have proven bioactive compounds. By a process of microencapsulation these bioactive compounds were encapsulated in the form of beads. Sodium caseinate and xanthan gum were mixed together to form the beads. This process helps to retain and protect the bio active ingredients from adverse reactions such as oxidation and nutritional deterioration. These microencapsulated beads were administered orally to 10 Oreochromis mossambicus the experimental fishes, with average body weight of 10-12 g and challenged against the pathogenic bacteria Aeromonas salmonicida to assess their antibacterial efficacy to control this bacterial pathogen. Microencapsulated bio active compounds were further characterized by FT-Raman, GC-MS, NMR, HPLC and SEM analysis. In this study, the effects of combined formulations of the different bioactive compounds were determined. Data obtained from the treatment of A. salmonicida infection in O. mossambicus using formulated bioactive compounds obtained from these seaweeds showed very high survival percentage in this species of fish.