Indigenous marine seaweeds and their biological activities have played a significant role in aquaculture especially with regard to their antibacterial and antiviral properties. The bioactive compounds and the toxicity profile of aqueous and ethanol extracts of Padina gymnospora and Sargassum cinereum species were assessed for the treatment of bacterial infection. The optimum exposure to seaweed extracts varied with different concentrations, from 100mg/l to 500mg/l of dried solvent extracts dispersed in 10l of water. It was found to be non-toxic up to 250mg/l. Oreochromis mossambicus infected with Pseudomonas aeruginosa showed abnormal activities like hyperactivity, lethargic movements, hemorrhagic lesions and exophthalmia, with LC 50 values of 1.287, 1.634 and 2.021mg/l for 72, 96, 120h respectively. They were exposed to sea weed extracts of different concentrations. Insignificant mortality was seen in the treated group. PCR and histopathological analysis were done. PCR studies were performed to study the distribution of P. aeruginosa in the tissues of different organs. The results revealed that PCR was positive for gills, while skin showed mild positive, which indicates the presence of the bacteria in these organs. The liver and the kidney were found to be negative.Statement of relevanceThe sea weed extracts are excellent source of antimicrobial compounds. These can be used for treating bacterial infection as an alternative to antibiotics which cause resistance. The extracts are found to be nontoxic and can be used in aquaculture industries for treating bacterial infection.