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 chelatant agent and Hg(II) (template). Hg(II)-imprinted polypyrrole (PPy) was also prepared on 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, however in the absence of any Hg2+ template. The strategy combining diazonium salt modification and ZnO nanorod decoration of gold electrodes permitted to increase considerably the specific surface and thus to improve the sensor performances. The limit of detection (LOD) of the designed sensor was ~1 pM, the lowest value ever reported in literature. 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. The Au-ZnO-IIP was found to be highly selective towards Hg(II) 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 enhance environmental quality.