The benzophenone, iriflophenone-3-C-glucoside, was isolated from Cyclopia genistoides using a combination of fluid-fluid extraction, high performance counter-current chromatography (HPCCC) and semi-preparative high performance liquid chromatography (HPLC). The microplate oxygen radical absorbance capacity (ORAC) assay, with fluorescein as probe, was adapted for use in an on-line HPLC configuration. The method was validated using a mixture of authentic standards including iriflophenone-3-C-glucoside, and the xanthones, mangiferin and isomangiferin. Trolox (6-hydroxy-2,5,7,8-tetramethylchroman-2-carboxylic acid) was included in the mixture for calculation of Trolox equivalent antioxidant capacity (TEAC) values. Using the on-line HPLC-ORAC assay, as well as 2,2-diphenyl-1-picrylhydrazyl (DPPH) and 2,2'-azinobis-(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS(+)) on-line assays, the antioxidant activity of iriflophenone-3-C-glucoside and isomangiferin was demonstrated for the first time. Iriflophenone-3-C-glucoside presented no radical scavenging ability against DPPH, but scavenged ABTS(+) and peroxyl radicals (TEACABTS of 1.04 and TEACORAC of 3.61). Isomangiferin showed slightly lower antioxidant capacity than mangiferin against DPPH (TEACDPPH of 0.57 vs. 0.62), but higher capacity against ABTS(+) (TEACABTS of 1.82 vs. 1.67) and peroxyl radical (TEACORAC of 4.14 vs. 3.69) than mangiferin. The on-line HPLC-ORAC assay was shown to be more sensitive for radical scavengers, but at the same time less selective for rapid radical scavengers than the DPPH assay.