Omija (Schizandra chinensis) is used as an ingredient in traditional medicine in East Asia. It is consumed as tea and wine and display pinkish-red color and beneficial physiological activity. However, the origin of Omija's unique color and bioactivity has not been studied extensively and its application is very limited. Thus, it was required to determine the chemical structure of major phenolic compounds of Omija fruit and evaluate their antioxidant activity. The colorants extracted from a domestic Omija cultivar were concentrated by a Sep-pak(R) Plus C(18) cartridge. A major high-performance liquid chromatography (HPLC) peak of anthocyan represented 94.1% of total absorbable compounds at 520 nm, which was further identified by LC-ESI-MS. The mass-to-charge ratio (m/z) of the major anthocyan was determined to be 727. Highly pure anthocyan fraction with a semipreparative HPLC was acid-hydrolyzed, and the sugar moieties linked to anthocyan (cyanidin) were characterized by thin layer chromatography (TLC) and high-performance anion exchange chromatography (HPAEC) analyses. The linkage patterns of sugars and core cyanidin structure were determined by (1)H- and (13)C-NMR analyses. Antioxidant activity of the extract and the purified anthocyanin was evaluated by 1,1-diphenyl-2-picrylhydrazyl (DPPH) and 2,2'-azino-bis(3-ethylbenzthiazoline-6-sulphonic acid) (ABTS) methods. As a result, the structure of the purified colorant was identified as Cya-3-O-xylrut. At the same molar level of the samples tested, the purified Cya-3-O-xylrut (31.2% and 39.2%) had substantially greater antioxidant activity than l-ascorbic acid (17.1% and 10.1%) from DPPH and ABTS methods, respectively. In this study, Omija colorant mostly consisted of Cya-3-O-xylrut explained 86% (DPPH) and 98% (ABTS) of total antioxidant activity derived from water extract from Omija.