The present study aims to evaluate some aspects of the pharmacoelectrochemistry of biflorin, a biologically active 1,2-naphthoquinone derivative, isolated from the roots of Capraria biflora. Electrochemical experiments involving biflorin using single, double-strand DNA and isolated bases had shown interaction of this quinone with DNA. Similar results were obtained using spectrophotometry (UV–Vis experiments and fluorimetry). Binding constants DNA–biflorin were obtained, through differential pulse voltammetry and fluorimetry. Spectroscopic studies and thermodynamic data had shown that biflorin can intercalate through dsDNA by van der Waals interactions and hydrogen bonds. The effects of biflorin–dsDNA interaction were addressed through a molecular cytogenetic approach, using comet assay and chromosome aberration induction evaluation. Indeed, biflorin, compared to the negative control, presented approximately 4- and 6-fold increases in DNA damage index and 4.1 and 13-fold enhanced damage frequencies at 40 and 80μM, respectively. However, biflorin did not significantly induce chromosome aberrations, suggesting that this molecule does not possess clastogenic potential, but cytotoxic potential. The absence of either clastogenic or aneuploidogenic activity of the compound reinforced its safety. Display omitted •The interaction of drugs with DNA is important in drug discovery and pharmaceutical development processes.•Biflorin is a very promising anticancer prototype.•Biflorin can intercalate through dsDNA by van der Waals interactions and hydrogen bonds.•Biflorin presents cytotoxic potential.•The absence of either clastogenic or aneuploidogenic activity reinforced the safety of biflorin.