Heavy metals, due to their inability to degrade, pose a serious environmental and nutritional problem. The accumulation of essential and non-essential heavy metals in living organisms reduces normal growth and development, resulting in acute poisoning, disease and even death of organisms. Melatonin is a very important multifunctional molecule in protecting plants from oxidative stress due to its ability to directly neutralize reactive oxygen species (ROS). Also, melatonin has a chelating property, which may contribute in reducing metal-induced toxicity. In this paper, the protective role of melatonin in counteracting metal-induced free radical generation was highlighted. Using the HPLC-FLD technique melatonin was identified and quantified in the roots and leaves of lemon balm (Melissa officinalis L.), grown under photoperiod conditions. Furthermore, the response of plants pre-treated with exogenous 0.1 mM melatonin to the increased zinc (Zn) and cadmium (Cd) concentrations was observed, with changes in mineral (Ca, Mg), physiological and antioxidant status of the plant during heavy metals stress. The obtained melatonin concentrations were the highest published for dry plants so far. Elevated Cd and Zn levels in soil caused alternation in biochemical and physiological parameters of lemon balm leaves and roots. However, melatonin pre-treatment increased plant tolerance to heavy metals stress. Increased Cd 3 and Zn uptake and their translocation into the leaves were also improved, indicating the possible use of melatonin in phytoremediation.