Food poisoning caused by bacterial agents is a worldwide problem, usually accompanied by unpleasant symptoms and may be sever leading to death. Natural compounds from marine algae namely flavonoids may play a role in the remedy of this condition. Aim: This research aims to assess the potency of flavonoids extracted from Enteromorpha intestinalis and Caulerpa prolifera as antibacterial agents. Methods: E. intestinalis was collected from Western Libyan Coast and C. prolifera was collected from Farwa Island. The antimicrobial activity and determination of minimum inhibitory concentration of algal flavonoid containing extracts was performed in vitro against some positive and negative Gram bacteria. Results: Crude extract containing flavonoids from E. intestinalis were more effective than C. prolifera extract against Staphylococcus aureus with antimicrobial essay (25-28+1 and 14.5-37.5+0.5-1.5), MIC (50 and 50-250 µg/mL), MBC (75 and 75-250 µg/mL). In Bacillus cereus, the antimicrobial assay (19-24.5+0.5-1.5: 24+1), MIC (50-250 + 100 µg/mL) and MBC (250 and 125 µg/mL). On the other hand, flavonoids containing extract from C. prolifera were more effective than E. intestinalis against Enterohemorrhagic Escherichia coli O157 EHEC O157 (25-28+1: 14-18.5+0.5-1.5), MIC (100-250:100-500 µg/mL) and MBC (150-250 and 250-500 µg/mL). Salmonella enterica qualitatively combat by flavonoid from E. intestinalis (13.5-14+0.5-1: 10.5-13.5+0.5-1.5), MIC (100-250: 250 µg/mL) and MBC (100-250: 250 µg/mL). Flavonoids from C. prolifera (4 strains: 2 strains) were effective against S. enterica. Crude flavonoids from both algae were not effective against Bacillus pumilus. Conclusion: Data from this study could conclude that flavonoid extracts from E. intestinalis and C. prolifera could be used against foodborne bacterial agents