Quality control methods for Cnidium officinale and Ligusticum chuanxiong are lacking because their quality is influenced by multiple factors. Thus, there is a need to develop a multifactorial method for measuring quality that is both standardized and practical. Here, we report a profiling method based on gas chromatography-mass spectrometry (GC-MS) to discriminate among the genetic varieties and agricultural origins of C. officinale and L. chuanxiong. Our metabolome analysis identified 68 metabolites, 13 of which were newly identified in our samples. The S-plot of the OPLS discriminant analysis enabled us to determine significant biomarkers. Using only double-compound biomarkers, the samples were successfully classified into distinct groups defined by genetic variety and cultivation origin. This method will simplify the process of searching for quality control markers that can be used to determine genetic variety and agricultural origin. (C) 2012, The Society for Biotechnology, Japan. All rights reserved.