AIM: To identify the medicine and search for new medicine resource at the molecular level, the ITS of "Zang Yin Chen"--Swertia mussotti and its adulterant species were sequenced.METHODS: The double-stranded DNA was amplified using PCR systems 9,600 kits and sequenced on an ABI 377 automated sequencer from both directions. RESULTS: The ITS sequences of S. mussotti in different populations showed no variation. It has the unique ITS sequence and shows distinct difference from its adulterant species. In the phylogenetic tree based on the ITS data of S. mussotti and all vicarious species constructed by Paup, S. franchetiana and S. mussotti clustered together with high bootstrap support. CONCLUSION: ITS sequences can be used for the molecular authentication between the S. mussotti and its adulterant species. S. franchetiana can be regarded as a new medicine resource of "Zhang Yin Chen".