Screening of biochemical compounds in marine algae is a gateway to understand the bioactive principles of antimicrobial activity and may be a significant tool in developing environment friendly herbicides and in drug discovery. In this study, the antibacterial activity of the seaweed Amphiroa anceps extracted with methanol and ethanol was determined against clinical isolates namely Vibrio cholerae 01 ogawa, Vibrio cholerae O139, Vibrio fluvialis, Vibrio parahaemolyticus, V. parahaemolyticus 81, V. parahaemolyticus O3:K6, salmonella enteritidis type 5, Enterotoxigenic E. coli, Bacillus cereus by disc diffusion method at different concentrations. Ethanolic extract showed the highest activity against V. parahaemolyticus, V. parahaemolyticus 81 and V. cholerae. The FTIR results showed the presence of major functional groups like amine, hydrogen bonded alcohols, alkanes and aromatic rings. Four major bioactive compounds were selected based on GC-MS data and used as ligands to dock in-silico against proteins of pathogenic bacteria that were used in antibiotic studies.