The metabolomic analysis of Ephedra species was performed using ¹H-NMR spectroscopy and multivariate data analysis. A broad range of metabolites could be detected by ¹H-NMR spectroscopy without any chromatographic separation. The principal component analysis used to reduce the huge data set obtained from the ¹H-NMR spectra of the plant extracts clearly discriminated three different Ephedra species. The major differences in Ephedra sinica, Ephedra intermedia and Ephedra distachya var. distachya were found to be due to benzoic acid analogues in the aqueous fraction and ephedrine-type alkaloids in the organic fraction. Based on this metabolomic recognition, one of nine commercial Ephedra materials evaluated was shown to be a mixture of Ephedra species. This method will be a useful tool for chemotaxonomic analysis and authentification of Ephedra species including quality control of plant materials.