Abstract: Peganum harmala seeds were sown in plastic pots in a greenhouse and seedlings were treated with Ni or Cu solutions at different concentrations (50, 100, 200, and 400 mg/kg) and without Ni or Cu solution (control). Ni or Cu accumulation, lipid peroxidation and the activities of antioxidative enzymes in the leaves and roots of P. harmala were examined and measured after Ni or Cu treatment. The Ni or Cu content in the leaves and roots of P. harmala increased in a dose-dependent manner. For Ni, the leaf was the preferential organ for metal storage, while for Cu, it was the root. Malondialdehyde content increased in the leaves and roots with the increase in Ni or Cu concentration, indicating lipid peroxidation increasingly aggravates with the stress. In the leaves of P. harmala, the activities of superoxide dismutase (SOD), catalase (CAT), peroxidase (POD), ascorbate peroxidase (APX) and glutathione reductase (GR) increased with the increase in Ni concentration, suggesting that together they play an important role in the ROS scavenging process, while in the roots, the activities of SOD, CAT and APX decreased, but POD and GR increased, suggesting both might play an important role in weakening Ni-induced oxidative damage. The five antioxidative enzymes increased as a whole in the leaves of Cu treated P. harmala, indicating they might be exerting a certain antioxidant function, protecting seedlings from Cu-induced oxidative damage. In the roots, APX activity was reduced, but the activities of SOD, CAT, POD and GR were enhanced, suggesting they could be effective in lessening Cu-induced oxidative damage.