Magainin 2 is pore-forming antimicrobial peptide on lipid matrix of bacterial membrane, secreted from the skin of the African clawed frog Xenopus laevis. The aim of this study was to investigate a new concept for antibacterial mechanisms called bacterial apoptosis-like cell death. We examined the morphological changes induced by magainin 2 in Escherichia coli, regarding apoptosis. Specifically, phosphatidylserine externalization from the inner to outer membrane surface was detected by Annexin V staining, and DNA fragmentation and chromatin condensation was detected by TUNEL and DAPI assay. We also found much mechanistic evidence to support the hypothesis that magainin 2 induces bacterial apoptosis-like death-including disturbance of membrane detected by DiBAC4(3), caspase activation observed by FITC-VAD-FMK staining, and analyzing the role of RecA in bacterial apoptosis-like death through the RecA expression assay by Western blot-in E. Coli when treated with magainin 2. On the basis of these results, magainin 2 exerts antibacterial activity with a new mechanism which is bacterial apoptosis-like death. Searching antimicrobial agents with novel mechanisms of action can be an effective strategy to coping with the emergence of new resistance mechanisms. Magainin 2 deserves further research as a potential antimicrobial therapeutic agent.