A biomimetic, ion-imprinted polymer (IIP) was prepared by electropolymerization of pyrrole at the surface of gold electrodes decorated with vertically grown ZnO nanorods. The vertical growth of the nanorods was achieved via an ultrathin aryl monolayer grafted by reduction of diazonium salt precursor. Pyrrole was polymerized in the presence of L-cysteine as chelating agent and Hg2+ (template). Hg2+-imprinted polypyrrole (PPy) was also prepared on a bare gold electrode in order to compare the two methods of sensor design (Au-ZnO-IIP vs. Au-IIP). Non-imprinted PPy was prepared in the same conditions but in the absence of any Hg2+ template. The strategy combining diazonium salt modification and ZnO nanorod decoration of gold electrodes permitted us to increase considerably the specific surface area and thus improve the sensor performance. The limit of detection (LOD) of the designed sensor was ~1 pM, the lowest value ever reported in the literature for gold electrode sensors. The dissociation constants between PPy and Hg2+ were estimated at [Kd1 = (7.89 ± 3.63) mM and Kd2 = (38.10 ± 9.22) pM]. The sensitivity of the designed sensor was found to be 0.692 ± 0.034 μA.pM-1. The Au-ZnO-IIP was found to be highly selective towards Hg2+ compared to cadmium, lead and copper ions. This sensor design strategy could open up new horizons in monitoring toxic heavy metal ions in water and therefore contribute to enhancing environmental quality.