A simple and cost-effective strategy for mercury ion sensing based on an easy and reliable colorimetric approach has been investigated by using L-cysteine functionalized gold nanorods (Au NRs). Detection tests have been performed on several ions, namely Hg2+, Zn2+, Cd2+, Cu2+, Pb2+ and As3+ and monitored by UV-Vis absorption spectroscopy, transmission electron microscopy (TEM) and infrared spectroscopy (ATR-FTIR). L-cysteine functionalized Au NRs have demonstrated a remarkable sensitivity for Hg2+ with limit of detection (LOD) at a few ppt level. A red-shift in the maximum of the typical longitudinal plasmon band of Au NRs has been observed and recognized related to aggregation phenomena occurring among functionalized Au NRs and triggered only by the presence of Hg2+ ions in solution. Interestingly, a significantly different response is recorded for the other tested ions. The results highlight that the functionalization of Au NRs with L-cysteine is an excellent route to implement a reliable colorimetric sensing device, able to push further down the LOD recorded for similar strategies based on spherical Au NPs.