Abstract Using UPLC and PDA detector, the fingerprints of Dendrobium devonianum and Dendrobium officinale produced in the Longling area of Yunnan Province, China were obtained quickly and efficiently, and 26 common peaks in Dendrobium devonianum and Dendrobium officinale samples were obtained by automatic peak matching through the “Chinese Medicine Chromatographic Fingerprint Similarity Evaluation System”. The relative peak areas of the common peaks were analyzed by PCA using R, and the results showed that Dendrobium devonianum and Dendrobium officinale could be well distinguished by PCA, which was consistent with the analysis results of OPLS-DA. The results fully demonstrate that Dendrobium devonianum and Dendrobium officinale grown in the same area can be effectively distinguished by using the method of common peaks combined with stoichiometry. The VIP value of the 13 common peaks is greater than 1.0, which has a significant contribution to the difference and it was differential marker in Dendrobium devonianum and Dendrobium officinale. At the same time, normal-phase silica gel column chromatography was used to separate and purify the compounds that are related to the common peaks, and a total of 7 compounds were identified, among which eupatolide and isoschaftoside belong to differential markers and characteristic compounds in Dendrobium devonianum and Dendrobium officinale, which have good biological health care activity. The successful identification of Dendrobium devonianum and Dendrobium officinale in Longling area of Yunnan Province and the discovery of related differential markers play an important role in the further research and development of Dendrobium devonianum as a new food raw material and its products.