The female sheep reproductive tracts were freshly collected from a local meat processing plant and used as experimental materials. Two antibacterial peptides were isolated and characterized from female sheep reproductive tracts by two consecutive chromatographic steps. The peptide isolation procedures included acetic acid extraction, dialyzed, gel filtration chromatography on Sephadex G-50, and reverse phase high-performance liquid chromatography (RP-HPLC). Their molecular mass were 4 820.47 u and 4 012.5 u, respectively, analyzed by MALDI-TOF-MS. The partial N-terminal amino acid sequences of two peptides were determined as AYVLDEPKP and YDSGA, respectively, by Edman degradation. The antimicrobial activity was tested during each purification step by the radial diffusion plate assay and broth microdilution method. These two peptides showed good antimicrobial activities against reference strains of G~+(S. Aureus ATCC2592 and Streptococcu ATCC55121), G~-(E. Coli ATCC25922) and fungi(C. Albicans ATCC2002). The peptides did not show active hemolytic activity against rabbit blood red cells and had no significant effects on human blood coagulation system. The discovery of antibacterial peptides in sheep reproductive system reveals that antibacterial peptides may play a role in innate immunity against microorganisms in a wide range of animal species.