Foodborne pathogens are one of the important biological hazards causing food spoilage. Nowadays, both research and industry are looking for natural sources of food preservatives and nutraceutical agents as an alternative of the chemical ones. Algae are one of these resources and they exist abundantly in the Egyptian aquatic environment. The algal biomass of Microcystis aeruginosa was used in the present study. Different solvents (deionized water, methanol, ethanol, acetone, chloroform, diethyl ether, ethyl acetate and hexane) were used for extraction the bioactive metabolites from M. aeruginosa. Diethyl ether extract (DEE) showed marked antibacterial activity against all tested foodborne pathogenic bacteria achieving inhibition ranged between 13.3 mm with K. pneumoniae and 29.3 mm with P. aeruginosa. The DEE extract of M. aeruginosa was fractionated using column chromatography technique. Among all fractions of diethyl ether extract, F7 had an effect against all tested bacteria. Eight compounds (9,12-Octadecadienoic acid methyl ester, Hexadecadienoic acid methyl ester, 9-Octadecadienoic acid, Nonadecane, Hexadecane, 9,12,15-Octadecadienoic acid, Octasiloxane and 10-Octadecenoic acid, methyl ester) were identified using GC/MS in such fraction. In addition to the antibacterial activity of DEE and F7, they worked as anticancer agents. Low concentration of DEE (