A new coumarin glycoside and a new glycoside of an acetylene derivative were isolated from the water-soluble portion of the methanolic extract of Atractylodes ovata rhizome together with eight known compounds. Their structures were characterized as scopoletin beta-D-xylopyranosyl-(1-->6)-beta-D-glucopyranoside and (2E)-2-decene-4,6-diyne-1,8-diol 8-O-beta-D-apiofuranosyl-(1-->6)-beta-D-glucopyranoside, respectively, based on chemical and spectroscopic investigations. A comparison of the polar constituents among Atractylodes japonica, Atractylodes lancea, and A. ovata is led to the conclusion that A. ovata is distinguishable from A. lancea and A. japonica, as also shown by phylogenetic analysis.