Abstarct: Agriculture faces many challenges such as climate change, urbanization, sustainable use of natural resources and environmental issues such as runoff, accumulation of pesticides and chemical fertilizers faces. In recent years, claims are indicative of the usefulness of nanotechnology in agriculture. In contrast some other reports are suggestive of the nanotoxicity on biological systems. Accordingly, we have evaluated the effect of magnesium oxide nanoparticles on the exxpression levels of genes involved in oxidative stress in soybean. The experiment was carried out in a hydroponic system using split plot in time with randomized complete block design in three replicates. Treatments were magnesium oxide nanoparticles on two levels (0.5 and 0.25 g/l), magnesium oxide at two levels (0.5 and 0.25 g/l) and control having no MgO. The results were suggestive of toxicity of nano-MgO through transcxript analysis of catalase, superoxide dismutase and peroxidase in cotyledon, leaf and root tissues via RT-PCR. The severe stress was noted at 0.25 g/l nano-Mg. In 0.5 g/l nano-MgO, toxicity was also observed. However, the severity of the up-regulation of genes were lower compared to 0.25 g/l nano-Mgo. It seems that tendency to agglomerate in higher concentration of nano-particles may in fact suppress their actual effect.