Abstract: The aim of this study was to see the effect of flavonoids quercetin and epicatechin on the transcript expression and activity of antioxidant enzymes. For this, tobacco seedlings were exposed to 50 and 100 μM quercetin and epicatechin for 21 days. The transcript expression level of various antioxidant enzymes like Glutathione-S-Transferase (GST), Glutathione Peroxidase (GPx), Ascorbate Peroxidase (APx), Glutathione Reductase (GR), Catalase (CAT) and Superoxide dismutase (SOD) were monitored in the root and shoot of exposed seedlings through reverse transcriptase PCR. The activity of these enzymes was studied spectrophotometrically. Interestingly, 50 μM epicatechin and 100 μM quercetin exposures were found to increase the expression of genes encoding antioxidant enzymes in shoot. In tobacco root, only Glutathione-S-Transferase (GST) and GPx expression was increased with 50 μM epicatechin and 100 μM quercetin exposures. Activity assay of all the enzymes showed similar trend to that of the transcript expression in shoot tissue. While in root, except CAT and SOD other enzymes activity also showed similar trend to that of expression pattern. Results have suggested the possible regulation of antioxidant enzymes by these two flavonoids at transcriptional and post-transcriptional level. Additionally, appropriate levels of such flavonoids seem to be essential for such regulations.