A liquid chromatography-electrospray ionization-ion-trap mass spectrometry (MS ) method was established and applied for authentication of Gentiana straminea from the four substitutes, G. tibetica, G. lhassica, G. waltonii and G. robusta, based on chemical profiling of the principal iridoid glucosides aided by a quadrupole time-of-flight mass spectrometry. The fragmentation pathways of the three representative iridoid glucosides, loganic acid, gentiopicroside and sweroside, were investigated by MS analysis in negative ion mode, which assisted the characterization of analogs detected in the chromatographic profiling of the tested Gentiana species. In total, 25 iridoids were identified or tentatively characterized from G. straminea and four substitutes, in which 7-O-(4''-O-glucosyl)coumaroyl-loganic acid and 7-O-coumaroyl-loganic acid are diagnostic in G. straminea and can serve as the proposed chemical markers to discriminate it from morphologically similar substitutes.