HPLC profile guided study led to the isolation of an acylated secoiridoid glycoside, named gentiotrifloroside (1), together with six known compounds, i.e., loganic acid (2), 6-O-beta-d-glucopyranosylgentiopicroside (3), swertiamarin (4), gentiopicroside (5), sweroside (6) and 2 -(o,m-dihydroxybenzyl)-sweroside (7) from Gentiana triflora and Gentiana rigescens. The structure of 1 was deduced from one- and two-dimensional NMR spectroscopic experiments. Compounds 1-7 were used successfully as chemical markers for the comparison of the four species of Gentiana used as Radix gentianae. Additionally, differentiation of Gentiana species mentioned and those used as adulterants was evaluated. The close similarity of chemical composition among the four genuine Gentiana species explain their popular usage as R. gentianae in Chinese medicine. We have also shown that the variation of chemical composition in R. gentianae and related adulterants agree well with their botanical phylogeny.