Gentiana crassicaulis Duthie ex Burk. and Gentiana macrophylla Pall. are two main sources of Radix Gentianae Macrophyllae (Qinjiao) available in markets, which has a wide range of anti‐inflammatory effects and has been extensively used for fighting rheumatoid arthritis. However, they vary in terms of chemical compositions, pharmacological activities, and biomass. In this study, a combined chemical and genetic (HPLC and DNA barcoding) approach was used to compare these two plants. Four predominant bioactive compounds, namely, gentiopicroside, loganic acid, swertiamarin, and sweroside, were used to assess the chemical variations. Based on chemical variations, 15 samples were clustered into two groups through PCA analyses. DNA barcoding utilizing the variable nuclear ITS2 regions were sequenced, aligned, and compared. Together with 61 sequences collected from GenBank, 76 batches of Qinjiao were clustered in two groups according to species origin. The genetic relationships indicated by the ITS2‐based NJ tree were consistent with the chemical variations. Thus, the chemical profiles determined by HPLC and DNA profiles obtained from ITS2 region could be applied for the quality control of Qinjiao.