Objective To identify the common Tibetan herb Dong-Na Duan-Chi by molecular pharmacognosy. Methods Ethnopharmacology investigation was carried out and local herbalists were visited to observe which plants were being used as Dong-Na Duan-Chi. Then, nuclear ribosomal DNA ITS sequences were amplified and sequenced for molecular identification. Results The botanic origins of Dong-Na Duan-Chi in Tibet Autonomous Region were authenticated as two species, i.e. Veronica eriogyne H.Winkl. and Veronica ciliata Fisch.. The sequences of ITS for Veronica eriogyne and Veronica ciliata are 551 bp and 552 bp in size. The results showed that nrDNA ITS sequences could be used to discriminate V.eriogyne and V.ciliata from closely related species. Conclusion nrDNA ITS sequences can be used as the molecular markers to identify the Tibetan herb Dong-Na Duan-Chi from other species of the same genus Veronica L.