Our previous studies showed that recombinant £]-bungarotoxin B chain exhibited membrane-damaging activity. Given that membrane-damaging activity is crucial for bactericidal effect of antibacterial peptide, the causal relationship between membrane-damaging activity and antibacterial action of B chain was performed in this study. £]-bungarotoxin B chain exhibited a growth inhibition on Escherichia coli (Gram-negative bacteria), but marginally displayed bactericidal effect on Staphylococcus aureus (Gram-positive bacteria). Destabilization of lipopolysaccharide (LPS) layer and inhibition of lipoteichoic acid (LTA) biosynthesis on cell wall increased bactericidal effect of B chain on E. coli and S. aureus. B chain induced leakage and fusion of bacterial membrane-mimicking liposomes. Compared with LPS, LTA notably suppressed membrane-damaging activity and fusogenicity of B chain. B chain showed similar binding affinity with LPS and LTA. Circular dichroism measurement revealed that LPS- and LTA-binding differently induced conformational change of B chain. Taken together, our data indicate that antibacterial action of B chain is related to its ability to induce membrane permeability and fusogenicity, and suggest that LTA- and LPS- induced conformational change of B chain affect membrane-damaging activity, fusogenicity and antibacterial activity of B chain.