<p>Ginseng (<i>Panax</i> species), are significant medicinal plants, have been utilized worldwide for their nutritional and therapeutic properties throughout history. While traditional cultivated ginseng is typically harvested after 6&#xa0;years, and harvesting earlier than 6&#xa0;years possess lower levels of ginsenosides. Recent technological advances have increased the use of in vitro techniques for production of ginseng biomass and ginsenosides via cell and/or adventitious root culture. Here, the metabolic profiles of a range of ginseng samples systems of cultivation ages, cultivars, and culture systems of in vitro-cultured and field cultivated ginseng were examined to determine whether Fourier-transform infrared (FT-IR) spectra combined with multivariate analysis of whole-cell ginseng extracts could be used for high-throughput sample discrimination. In total, 26 ginseng samples belonging to four categories were analyzed by principal component analysis (PCA) and partial least squares discriminant analysis (PLS-DA). Dendrograms based on hierarchical cluster analysis (HCA) of the ginseng sample spectral patterns showed that cultivation ages and culture systems were readily clustered into two subgroups in a polysaccharide spectrum-dependent manner. The sample group containing in vitro cell and organ samples was segregated into four subgroups in a nucleic acid spectrum-dependent manner. These results indicated that FT-IR spectroscopy combined with multivariate statistical analysis of in vitro and ex vitro ginseng could be used as an alternative method for metabolite discrimination. Consequently, PLD-DA analysis of FT-IR metabolic fingerprinting data could serve as a valuable tool for screening bioactive compounds and exploring metagenomic relationships in ginseng research.</p>