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The chemical investigation of ethanolic extract from Swertia mussotii Franch. has resulted in the isolation of 11 compounds which were identified as Orcinol-β-D-glucoside (1), Shamimin (2), Mangiferin (3), Decussatin (4), Bellidifolin (5), Desmethylbellidifolin (6), Protocatechuic acid (7), 1,7-Dihydroxy-3,8-dimethoxyxanthone (8), 1,8-Dihydroxy-3,5-dimethoxyxanthone (9), 1-Hydroxy-3,5-dimethoxyxanthone (10), Telephioidin (11). The chemical structures of these compounds were identified by a combination of spectroscopic analysis and a comparison with those reported in literature. Among them, compounds 1, 2, 7 and 11 were isolated from the genus Swertia for the first time. Moreover, the chemotaxonomic significance of these compounds was summarised. The chemotaxonomic study suggests that there is a close chemotaxonomic relationship between S. mussotii and other species of Swertia, such as S. punicea, S. macrosperma, S. japonica, S. phragmitiphylla, S. chirayita, S. cordata and S. binchuanensis, with presence of compounds 3~6, 8~10. The xanthones and their glycosides may sever as important chemotaxonomic markers of Swertia genus.