Definitive identification of original plant species is important for standardizing herbal medicine. Although only the dried roots of Cynanchum wilfordii (Asclepiadaceae) are prescribed as Cynanchi Wilfordii Radix in Korean Pharmacopoeia, the roots of C. wilfordii and C. auriculatum are often misused in the Korean herbal market due to their morphological similarity and similar name. Therefore, it would be very useful to discover an effective chemical marker for the identification of the two species. To this end, we carried out a phytochemical study on the roots of C. wilfordii. As a result, twenty compounds were isolated from the roots of C. wilfordii and their chemical structures were identified as β-sitosterol (1), wilfoside C1N (2), wilfoside C3N (3), wilfoside K1N (4), methyleugenol (5), wilfoside C1G (6), cynauriculoside A (7), daucosterol (8), 2,4-dihydroxyacetophenone (9), cynandione A (10), 2,5-dihydroxyacetophenone (11), acetovanillone (12), p-hydroxyacetophenone (13), sucrose (14), conduritol F (15), geniposide (16), succinic acid (17), 3-(β-D-ribofuranosyl)-2,3-dihydro-6H-1,3-oxazine-2,6-dione (18), bungeiside A (19), cynanoneside B (20). Among them, compounds 15, 16, 18, 19, and 20 were isolated for the first time from this species. Furthermore, conduritol F (15) was demonstrated to be contained only in C. wilfordii. Therefore, it may be useful as a chemical marker to identify the two species C. wilfordii and C. auriculatum.