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Saposhnikoviae Radix (SR) is a commonly used crude drug that is obtained from the root and rhizome of Saposhnikovia divaricata which is distributed throughout China, Korea, Mongolia, and Russia. To evaluate the quality of Mongolian S. divaricata, metabolomic profiling of 43 plant specimens from different regions of Mongolia, as well as 8 SR samples and 2 plant specimens from China, were conducted by liquid chromatography-ion-trap-time-of-flight-mass spectrometer (LC-IT-TOF-MS). LC-MS profiles of the specimens showed uniformity and 30 compounds were tentatively identified, including 13 chromones and 17 coumarins. Among them, 16 compounds were isolated and unambiguously verified by comparing them with the spectroscopic data of standard compounds. Orthogonal partial least squares-discriminant analysis (OPLS-DA) based on LC-MS data from 7 Mongolian specimens and 8 Chinese SR samples as well as 2 plant specimens revealed that these 2 groups were clearly distinguishable and that Mongolian specimens were characterized by an abundance of prim-O-glucosylcimifugin (1). Moreover, the OPLS-DA of the Mongolian specimens showed that they can be discriminated by their growing regions based on the content of 8 chromones. The total content of dihydrofurochromones 1-3 was relatively higher in the specimens from Khalkhgol in the far eastern part of Mongolia, while contents of 10, 11, 15, and 16 were higher in those from Holonbuir in the eastern part. Based on this research, the roots of S. divaricata from Mongolia have potential as a new resource of SR in Kampo medicine.