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Thidiazuron [N-phenyl-N-(1, 2, 3-thidiazol-5-yl) urea, TDZ] treatment significantly improved shoot morphogenesis of Saussurea involucrata Kar. Et Kir (S. involucrata) leaf explants. The biochemical mechanisms underlying TDZ-induced shoot organogenesis were investigated by measuring endogenous plant growth hormones, H2O2, as well as the activities of superoxide dismutase (SOD) and catalase (CAT). The levels of endogenous gibberellic A3 (GA(3)) and zeatin (ZT) significantly increased in leaf explants subject to a 28-day treatment than the controls. However, extending exposure time to TDZ inhibited GA(3) accumulation. At the same time, the SOD activity increased significantly until the 28th of TDZ treatment time and the CAT activity reduced simultaneously, which was closely linked with the significant increase in H2O2 concentrations in the explants. And there was a sharply promotion after the 35 day of culture time if the plant tissue was always in medium contained, which was in company with the cell activity decreased. We propose that a combination of increased GA(3), ZT, and H2O2 concentration is the basis for the enhanced shoot morphogenesis in response to TDZ treatment. These results provide a starting point for an improved understanding of the biochemical mechanisms underlying TDZ-induced shoot organogenesis of S. involucrata.