A series of mononuclear copper(II) complexes [Cu(bdmpe/bpmpe)X]Y [bdmpe= N,N‐bis((3,5‐dimethyl‐1H‐pyrazol‐1‐yl)methyl)‐2‐(phenylthio)ethan‐1‐amine, Y=PF6−, X=Cl 1, Br 3 and Y=BF4−, X=Cl 2, Br 4; bpmpe=N,N‐bis((1H‐pyrazol‐1‐yl)methyl)‐2‐(phenylthio)ethan‐1‐amine; Y=PF6−, X=Cl 5, Br 7 and Y=BF4−, X=Cl 6, Br 8] have been synthesized by the reaction of copper halides with ligands bdmpe/bpmpe in presence of Y and characterized. Single crystal X‐ray crystallography study indicates that complexes are mononuclear with distorted square pyramidal geometry. Complexes 1 and 7 show supramolecular dimeric nature due to short intermolecular interactions. The antimicrobial activity of all complexes were investigated against Gram positive (Bacillus subtilis, Streptococcus aureus) and Gram negative (Escherichia coli, Pseudomonas aeruginosa) bacterial strain by agar well dilution method and have demonstrated significant antimicrobial activity of the compounds. The studies on the interaction of complexes and DNA by agarose gel electrophoresis method revealed that the complexes can effectively cleave the circular plasmid DNA at very low concentrations.