The quercetin diglycoside: Quercetin 3-O-β-D-glucopyranosyl-7-O-α-L-rhamnopyranoside (1) and kaempferol tetraglycoside: Kaempferol-3-O-α-L-[2-O-β-D-(6-p-feruloyl)3-O-β-D-(6-p-coumaroyl)glucopyranosyl]-rhamno pyranosyl-7-O-α-L-rhamnopyranoside (2), were isolated by various chromatography methods from the stem of Cleome viscosa L. and Cleome chelidonii L.f., respectively. Their chemical structures were eclucidated by HR-ESI-MS, 1D- and 2D-NMR experiments and their NMR data were compared with analogies previous reported data. The methanol fraction extracts of the stem of Cleome viscosa L. and Cleome chelidonii L.f. were also examined hepatoprotective activity on carbon tetrachloride (CCl4) induced toxicity of liver in mice for 8 weeks. The result showed that at the dose of 30 mg/kg and 45 mg/kg, the methanol extract of those decreased ALT and AST concentration significantly in comparision with extract-untreated group and the hepatoprotective effect of this extract could be comparable to that of silymarin, a hepatoprotective compound against hepatotoxicity of various chemicals. The results of the present study indicated that Cleome viscosa L. and Cleome chelidonii L.f. are a potential source for natural hepatoprotection.