Aquatic organisms are a rich source of novel and bioactive compounds. Cyanobacteria and microalgae being a rich source of bioactive compounds have recently found immense application in human and animal medicine. The present study was attempted to find out the effect of the various extracts of Spirulina platensis, Chlorella vulgaris, Saragassum wightii and Saragassum latifolium using different solvents (methanol, ethanol, ethyl acetate and chloroform) as antimicrobial agents against five bacterial pathogens; S. aureus, E. coli, P. aeruginosa, Salmonella sp, Shigella sp. Results indicate that among the various extracts used, methanol extracts of tested cyanobacterial and algal species appeared to be the most effective ones showing maximum antibacterial activity against the selected bacterial pathogens. Spirulina platensis appeared to be the most effective against all the pathogens studied. The antibacterial substance was purified using column chromatography. The nature of the purified active fractions was detected using different chemical analyses (UV, FT-IR, 1H NMR and GC-MS) which indicated that it is an aliphatic compound and has different active groups (-OH,-C=O,-CH2 and –CH3). The results of this investigation proved that the tested cyanobacterium could be a good source for the production of promising antimicrobial agents.