A number of biologically active complexes of cobalt(II) and nickel(II) with pyrazinedicarboxaimido derived thienyl and furanyl compounds having the same metal ion but different anions such as sulphate, nitrate, oxalate and acetate have been synthesized and characterized on the basis of their physical, spectral and analytical data. In order to evaluate the role of anions on their antibacterial properties, these ligands and their synthesized metal complexes with various anions have been screened against bacterial species Escherichia coil,Pseudomonas aeruginosa and Staphylococcus aureus. The title studies have proved a definitive role of anions in increasing the antibacterial properties.