•The ruthenium(II) complex (RuTh) can against both the G − bacteria E. coli and the G + bacteria S. aureus.•The RuTh is more toxic to S. aureus than that to E. coli.•RuTh against bacteria through disrupting bacterial cell wall integrity and its cellular componentsMetal based drug represents a novel group of antimicrobial agents with potential application for the control of bacterial and fungal infections. In this study, we fabricate ruthenium(II) complex containing the polypyridyl ligands, namely [Ru(phen)2(tip)] (ClO4)2 (RuTh) and carefully investigate its antibacterial activities against both the Gram-negative (G −) bacteria Escherichia coli (E. coli) and the Gram-positive (G +) bacteria Staphylococcus aureus (S. aureus). The RuTh is more toxic to S. aureus than that to E. coli. The antibacterial effects of RuTh are further investigated, revealing specific mechanisms. The results demonstrate that RuTh functions as a bactericide against the E. coli and S. aureus through disrupting bacterial cell wall integrity and its cellular components.We fabricate ruthenium(II) complex containing the polypyridyl ligands, namely [Ru(phen)2(tip)] (ClO4)2 and carefully investigate its antibacterial activities against both the Gram-negative bacteria E. coli and the Gram-positive bacteria S. aureus.