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This study aimed to determine the role of sulfhydryl compounds in the subcells of C. rupestris under Pb stress. Different concentrations (0, 0.5, 1.0, 2.5, 5.0, 7.5, and 10 mg/L) and different exposure days (1, 3, 5, and 7 days) were designed to analyze the subcellular distribution of non-protein thiols (NPT), glutathione (GSH), and phytochelatins (PCs) in C. rupestris. NPT, GSH, and PCs increased significantly with increasing Pb stress in the cell wall and soluble fraction, especially NPT. NPT and GSH slowly increased, and PCs showed