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Fatty acid methyl esters (FAME) derived from lipids of microalgae is known to have wide bio-functional materials including antimicrobials. FAME is an ideal super-curator and superior anti-pathogenic. The present study evaluated the efficiency of FAME extracted from microalgae Scenedesmus intermedius as an antimicrobial agent against Gram positive (Staphylococcus aureus, Streptococcus mutans, and Bacillus cereus) Gram negative (Escherichia coli and Pseudomonas aeruginosa) bacteria and Fungi (Aspergillus parasiticus and Candida albicans). The minimal inhibitory concentration (MIC) for the gram negative bacteria was determined as 12–24 μg mL−1, whereas MIC for gram positive bacteria was 24–48 μg mL−1. MIC for the fungi was as high as 60–192 μg mL−1. The FAME profiles determined by gas chromatography showed 18 methyl esters. Among them, pharmacologically active FAME such as palmitic acid methyl ester (C16:0) was detected at high percentage (23.08%), which accounted for the bioactivity. FAME obtained in this study exhibited a strong antimicrobial activity at the lowest MIC than those of recent reports. This result clearly indicated that FAME of S. intermedius has a strong antimicrobial and antioxidant property and that could be used as an effective resource against microbial diseases.