Abstract A cathodic adsorptive electrochemical behavior of cytosine and guanine in the presence of acridine orange (DNA‐intercalating dye) at the static mercury drop electrode was investigated. Optimum experimental conditions were found to be the use of a 0.001 M NaOH solution with an acridine orange concentration of 2 ppm, an initial potential of −0.0 V, a scan rate of 10 mV s−1, and a linear scan mode. The more convenient relation to measuring the cytosine and guanine in the presence of acridine orange is 1:1:2. A new approach for improving the selectivity in analysis using copper and zinc as masking agents also was investigated. Cyclic voltammetry was used to characterize the interfacial and redox behavior.