Liquid chromatography coupled to negative electrospray ionization (ESI) tandem mass spectrometry (MS/MS) employing a time-of-flight tandem mass spectrometer was used in the structural determination of phenolic compounds and sesquiterpenoids occurring in the extract from Artemisia rupestris L. A total of 91 compounds including chlorogenic acid derivatives, flavonoids (aglycone, O-glycosyl, C-glycosyl and C,O-glycosyl), 2-phenoxychromones and guaiane sesquiterpenoids were identified by comparing the retention time and fragmentation behavior with reference standards or according to accurate mass measurement and the characteristic fragmentation at low and high collision energy. Most of these compounds were reported in Artemisia rupestris L. for the first time. Meanwhile, the proposed pathway and the major diagnostic fragmentation of 2-phenoxychromone and rupestonic acid were investigated to trace 2-phenoxychromone and rupestonic acid derivatives in crude plant extracts. According to these rules, we have successfully characterized five potential novel compounds including three 2-phenoxychromones (6-demethoxy-4′-O-methylcapillarisin-O-hexosylglucuronide, 6-demethoxy-4′-O-methylcapillarisin-O-pentosylhexoside and 6-demethoxy-4′-O-methylcapillarisin-O-deoxyhexosylhexoside) and two sesquiterpenoids (hexosyl-glycurinide-rupestonic acid and hexoside-rupestonic acid). Copyright © 2011 John Wiley & Sons, Ltd.