Background: Fatty acid profiling has been widely used in the bacteria species identification, we hypothesized that fatty acid characteristics might discriminate the Panax herbs according to species. To test the hypothesis, fatty acids of Panax species, including Panax ginseng, Panax notoginseng and Panax quinquefolius, were characterized and compared using gas chromatography-mass spectrometry (GC-MS) followed by multivariate statistical analysis.Results: The content of investigated 11 fatty acids, including myristic acid, pentadecanoic acid, palmitic acid, palmitoleic acid, heptadecanoic acid, stearic acid, oleic acid, linoleic acid, α-linolenic acid, arachidic acid and eicosadienoic acid, obviously varied among three species, suggesting each species has its own fatty acid pattern. Principal component analysis and hierarchical clustering analysis according to the absolute and relative contents of fatty acids, showed that 30 tested samples could be clearly differentiated according to the species.Conclusions: These findings demonstrated that GC-MS-based fatty acid profiling coupled with multivariate statistical analysis provides reliable platform to classify these three Panax species, which is helpful for ensuring their safety and efficacy.