Dried methanol extract of Hypericum hyssopifolium subsp. elongatum var. elongatum was dissolved in distilled water, and then fractioned by re-extracting with petroleum ether, chloroform, and ethyl acetate, subsequently. Antioxidant and 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical-scavenging activities of these fractions were determined, in vitro. The amounts of total phenolic compounds were also determined. None of these fractions showed antioxidant activity, in contrast water and ethyl acetate fractions acted as prooxidant. However, the ethyl acetate fraction exhibited the highest DPPH radical-scavenging activity and the amount of its total phenolic compound was highest, too. Therefore, ethyl acetate fraction was subjected to further separation by chromatographic methods. Thus, five flavonoids (I3,II8-biapigenin, quercetin, quercetin-3-O-alpha-L-arabinofuranoside, quercetin-3-O-beta-D-galactopyranoside, quercetin-3-O-beta-D-galactopyranoside-7-O-beta-D-glucopyranoside) and a napthodianthrone (hypericin) were isolated, and their structures were determined by UV, IR, NMR, and MS spectroscopic methods. All isolated compounds showed antioxidant and DPPH radical-scavenging activities. Although, I3,II8-biapigenin and hypericin were able to show highest antioxidant activity, they had the lowest DPPH radical-scavenging activities. From these results, it can be suggested that these compounds may be used as potential antioxidants. In addition, the petroleum ether fraction was subjected to silica gel column chromatography (CC). Then, n-dotriacontanyl hexadecanoate, bis(2-methylheptyl) phthalate, and beta-sitosterol were isolated from it. It is of interest to present the spectral data of bis(2-methylheptyl) phthalate first time in the present study.