Eucheuma cottonii is a valuable marine algae species widely cultivated in Sumenep, Madura. Recent research on the biochemical characterization of various marine algae species has identified active anti-microbial polyphenols and their derivatives, such as flavonoids. These compounds possess anti-inflammatory and anti-microbial properties. Organisms with sufficient levels of polyphenols and flavonoids tend to have an enhanced immunity against bacterial and viral infections. As a result, Eucheuma cottonii has the potential to serve as a natural source for new medicines derived from the marine resources of Madura Island. This study aimed to optimize the use of marine biological resources, specifically Eucheuma cottonii, as the main ingredient for anti-microbial drugs. The research was conducted between May and November 2021 at the Integrated Laboratory of the University of Trunojoyo Madura. The stages of the research included sampling Eucheuma cottonii, extracting its active compounds, and testing the anti-microbial activity against Aeromonas hydrophila. The results showed that the average yield of Eucheuma cottonii extract ranged from 2.978% to 3.296%. The extract demonstrated anti-microbial properties, as evidenced by the formation of inhibition zones in Aeromonas hydrophila colonies.