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The Scanning electrochemical microscopy (SECM) is used to selectively detect intervening mismatches and abasic sites within monolayers of ds-DNA self-assembled onto gold electrodes. The electrocatalytic cycle involving oxidation of leucomethylene blue (LB), an electrochemically reduced form of methylene blue intercalated within the ds-DNA monolayer self-assembled on gold electrode, by the SECM tip-generated ferricyanide allows regeneration of LB via long-range heterogenous electron transfer mediated by the DNA p-stack. Monolayers featuring disruptions in the DNA p-stack via a single-base mismatch or abasic site exhibit strongly attenuated methylene blue electrochemistry within the DNA film leading to a disruption of the catalytic cycle, thereby diminishing the SECM tip current. The inherent differences in catalytic tip currents can be used to distinguish monolayer domains containing native ds-DNA versus ds-DNA containing p-stack lesions within the micron-level lateral spatial resolution of SECM.