Antimicrobial peptides are widely found in living organisms and are known to play a critical role in innate immunity. Numerous antimicrobial peptides from diverse species appear to be effective against pathogenic microorganisms of bacteria, fungi, protozoa, and viruses. Because antibiotic resistance is a global health issue in the fight against pathogenic microorganisms, there has been an urgent need for development of new antibiotic substances. In the current study, we performed yeast two hybrid screening using Beclin1 bait in order to find new peptide antibiotics from a random peptide library. Two candidate peptides from the screening were expressed in a yeast secretory system of Pichia pastoris and tested for any antimicrobial activity against Staphylococcus aureus, MRSA, MRSA2242, MRSA2250, Lactobacillus casei, and Lactobacillus acidophilus. Disc clear zone assay and spectrophotometric analysis revealed that the two peptides exert a decent activity against the pathogenic bacteria, in contrast to minimal effect on the commensal Lactobacillus strains. Taken together, this study presents novel peptides with antibacterial activity against the pathogenic forms of Staphylococcus aureus and suggests the possibility that these peptides, upon further characterization, may be developed as clinically useful antibiotics.