Objective: To identify Stephaniae Tetrandrae Radix and its adulterants based on internal transcribed spacer 2 (ITS2) and its secondary structure. Method: Total 36 ITS sequences were downloaded from GenBank and aligned by Geneious R11.0.3. The intraspecific and interspecific K2P genetic distance was calculated by MEGA 7.0

and the neighbor joining (NJ) phylogenetic tree was built by the same software.Simultaneously

the secondary structure of each sample was predicted by the ITS2 Database online softwareand aligned by 4sale software. Finally

ProfDistS software was used to construct the profile neighbor-joining (PNJ) phylogenetic tree based on the distance method. Result: The average interspecific genetic distance was far greater than the average intraspecific genetic distance. NJ tree showed that Stephaniae Tetrandrae Radix and its adulterants were clustered into 6 branches;both Stephaniae Tetrandrae Radix and its adulterants had different secondary structures. The PNJ tree showed more branches and higher resolution than NJ tree. Conclusion: ITS2 can be used as a DNA barcode for distinguishing Stephaniae Tetrandrae Radix from its adulterants

but the identification results would be more accurate when considering the phylogenetic information contained in ITS2 secondary structure.