Abstract: Bactrian camel milk and whey protein of cow milk were hydrolyzed by pepsin. The hydrolysate was separated and purified by ultrafiltration and dextran gel chromatography. Bacteriostatic activity,concentration of protein tested by bisquinoline carboxylic acid method(BCA),the relative molecular mass,and the amino acid composition of the obtained protein peptide were determined. The results showed that the polypeptide fragment(F3)of the molecular weight<3 kDa of camel milk and cow milk obtained by ultrafiltration,had the strongest antibacterial activity,the purity of camel milk G-25-2 and cow milk G-25-2 components obtained by chromatography of the F3(<3 kDa)component was higher(protein concentrations were 95.60% and 95.32%,respectively);camel milk G-25-2 and cow milk G-25-2 components had antibacterial activity against Escherichia coli and Staphylococcus aureus,and the minimum inhibitory concentration was 32.50 and 65.00 mg/mL respectively. Amino acid analysis showed that the content of total basic amino acid and total hydrophobic amino acid in the high activity antimicrobial peptide was the highest,32.80% and 65.76% respectively in camel milk G-25-2,and 31.77% and 58.70% respectively in cow milk G-25-2.The research result showed that camel milk and cow milk had similar antibacterial effect and the ability was higher than cow milk,which provided a theoretical reference for further research on camel milk bacteriostatic peptide.