Abstract:[Objective] To investigate the antimicrobial mechanism of DNA action of CecropinA-Magainins treatment on the Methicillin-resistant Staphylococcus aureus (MRSA). [Methods] The mechanism was analyzed by Confocal Laser Scanning Microscope (CLSM), Gel shift Assay, Ultraviolet Spectrum Analysis and Fluorescence Spectrum Analysis. [Results] The results demonstrated that the minimal inhibitory concentration (MIC) of the peptide against MRSA was 64 mg/L. The hybrid peptide could accumulate within the bacterial cell, and bind with the genomic DNA in vitro. Meanwhile, the hybrid peptide caused the change of DNA conformation. The results of Fluorescence Spectrum Analysis showed that the hybrid peptide competitively embedded genomic DNA with EB, and its combination mode was similar to the mode of EB and DNA. Finally, we found the combination mode of hybrid peptide and DNA was mixed mode. [Conclusion] CecropinA-Magainins can enter into the bacterial cell, bind with the genomic DNA. The hybrid peptide kills bacteria via intracellular-targeting mechanism.