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Agricultural crops are an essential base component of all ecosystems and it is important to assess the impact of nanoparticles on them and the risks involved. In this study we have investigated the impact of the different concentrations (ppm) of citrate stabilized gold nanoparticles (GNPs) ranging from 100 to 400 on physiological and biochemical parameters of the seedlings of Brassica juncea as a model oil crop system. GNPs were synthesized and characterized through Uv-visible spectra and transmission electron microscopy. The qualitative accumulation of GNPs into seedlings of Brassica juncea was ascertained through cyclic voltammetry and Laser Induced Breakdown Spectra (LIBS). Exposure of GNPs caused a decrease in overall growth of Brassica juncea was attributed to increase in free radical stress, supported by a general increase in biomarkers such as antioxidative enzymes, proline and hydrogen peroxide due to the formation of reactive oxygen species.