Objective: To investigate the differences between main secondary metabolites and molecules of Gentiana rigescens from different populations by the method of content determination and DNA barcoding analysis. Method: An HPLC method was applied to determine the contents of gentiopicroside

swertiamarin

sweroside and amarogentin in G. rigescens roots and rhizomes

stems

leases

and flowers

and the HPLC fingerprint was established

the main secondary metabolites were evaluated by one-way ANOVA

and the DNA barcoding technique was used to test ITS2 sequences of G. rigescens. Result: There were significant differencedifferences in the contents of gentiopicroside

swertiamarin

sweroside and amarogentin (P<0.01) in different parts.fractions. The results of ITS2 sequences showed that there was no significant difference in the molecule of G. rigescens from different populations. Conclusion: There was differences in main secondary metabolites of G. rigescens from different populations

but there was little difference of with less differences among molecules and a close genetic relationship.