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Seeds aqueous extracts from Litchi chinensis and Nephelium lappaceum were investigated for antibacterial activity by disc diffusion method and protein profile. Both seed aqueous extracts show moderate inhibition against pathogenic bacteria, both gram positive including Staphylococcus aureus, Streptococcus pyogenes, and Bacilllus subtillis and gram negative bacteria including Escherichia coli and Pseudomonas aeruginosa. Overall analysis of the antibacterial activity of tested samples revealed that the highest inhibitory activity was produced by Litchi chinensis (15 ± 0.55 mm) against S. pyogenes. Tris glycine SDS PAGE revealed major protein band approximately 15.5 kDa and 22-kDa. Protein contents of Seeds of Litchi chinensis and Nephelium lappaceum were approximately 7.5 and 13.5 mg/g, respectively.