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[Display omitted] • An electrochemical DNA biosensor has been effectively developed based on polyacrylic microspheres and gold nanoparticles (AuNPs) for the identification of the gene sequence of the harmful microalgae Alexandrium minutum. • Anthraquinone-2-sulfonic acid derivative (AQMS) works as a specific indicator for redox DNA hybridisation, enabling the identification of the harmful microalgae Alexandrium minutum for the first time. • The DNA biosensor, employing AQMS as a redox label for the detection of Alexandrium minutum demonstrated a minimal limit of detection and possessed an extensive linear range. • This new production of an electrochemical biosensor serves as a straightforward and rapid instrument for identifying Alexandrium minutum DNA in water samples tainted with this detrimental algae. Alexandrium species, including Alexandrium minutum (A. minutum) , are capable of producing paralytic shellfish toxins, which frequently adversely affect the aquaculture and fishing industries. Since it's critical, it needs to be precisely detected. This study addresses the development of an electrochemical DNA biosensor for detecting toxic microalga A. minutum gene sequence based on anthraquinone-2-sulfonic acid derivative (AQMS) as the redox DNA hybridisation indicator. DNA binding studies using UV–Vis and molecular docking were performed, confirming the intercalation behaviour. The binding constant (K b) of such interaction was 4.5 × 105 M−1 with the hyperchromicities shown are 13 % and 18 %, and the relative binding energies of the docked AQMS towards DNA was − 8.3 kcal mol−1. The RMSD value for AQMS was 0.2 Å, underscoring a remarkably close alignment and similarity with the redocked structure. The aminated DNA probe was then immobilised onto the screen-printed carbon electrode (SPCE) containing polyacrylic microspheres and gold nanoparticles (AuNPs). An excellent linear relationship of the response to DNA concentrations was obtained from 1 × 10−15 M to 1 × 10−5 M (R2 = 0.9908) with a limit detection (LOD) at 6.91 × 10−14 M. This lower detection limit is a significant improvement over several other electrochemical biosensors reported so far for A. minutum determinations. Selectivity experiments demonstrated that this new voltammetric DNA biosensor could distinguish between A. minutum target and non-target DNA and can regenerate after use for up to two cycles. This DNA biosensor has demonstrated its ability to early detect toxic microalgae by effectively differentiating among various non-target dinoflagellate species. Furthermore, the biosensor has been shown to successfully identify A. minutum in water samples from a river in Tumpat, Kelantan, with results comparable to standard polymerase chain reaction (PCR). [ABSTRACT FROM AUTHOR]