Species of herbaceous flowering perennial plant of the family Campanulaceae such as Platycodon grandiflorum (P. grandiflorum) and Codonopsis lanceolata (C. lanceolata) widely used in traditional medicine to treat different diseases. In spite of different medicinal results after consumption of the plants, it is hard to distinguish between two of them, because of their similar morphological characteristics. In this study, a gas chromatography-mass spectrometry (GC-MS) - based metabolite profiling approach was performed and examined to discriminate tuberous roots of P. grandiflorum and C. lanceolate for medicinal purposes. Two basic approaches for sample preparation, headspace solid-phase microextraction (HS-SPME) and solvent extraction were adopted. Multivariate statistical techniques, such as orthogonal partial least-squares discriminant analysis (OPLS-DA) plots showed significant differences between P. grandiflorum and C. lanceolata for polar primary and volatile organic metabolites. A number of potential candidates were suggested as the chemomarkers for discrimination of two plants.