Cibotii Rhizoma, the dried rhizome of Cibotium barometz J. Smith (C. barometz), has long been used to treat bone or nervous system disorders. In this regard, we isolated three main phenolic compounds, onitin-4-O-${eta}$-D-glucopyranoside (1), irisdichototins E & F epimeric mixture (2), and protocatechuic acid (3) from C. barometz methanol extract. In addition, we screened their antioxidative activities by DPPH, ABTS radical, and superoxide scavenging assays. Among these three compounds, irisdichototins E & F and protocatechuic acid showed strong antioxidant activities. Also, the antioxidant activities of the C. barometz extracts were proportional to the contents of irisdichototins E & F and protocatechuic acid, thus these two phenolic compounds could be main active compounds of C. barometz. In addition, onitin-4-O-${eta}$-D-glucopyranoside is considered as a marker compound of C. barometz because this compound is specifically contained in C. barometz which belongs to Pteridophyta order. A rapid analysis method for the simultaneous determination of phenolic compounds was also developed by UPLC (Ultra Performance Liquid Chromatography). Using the developed method, the two active compounds (irisdichototins E & F and protocatechuic acid) and a marker compound (onitin-4-O-${eta}$-D-glucopyranoside) were successfully quantified in 14 commercial samples that were collected from different regions.