Spectral fingerprints of samples of three Panax species (P. quinquefolius L., P. ginseng, and P. notoginseng) were acquired using UV, near-infrared (NIR), and MS. With principal component analysis, all three methods allowed visual discrimination among the three species. All three methods were able to discriminate between white and red ginseng, and showed distinctive subgroupings of red ginseng related to root quality (age/size). Analysis of variance was used to evaluate the relative variance arising from the species, run, and analytical uncertainty, and was used to identify the most information-rich portions of the spectrum for NIR and UV. Accurate classification of the three species was obtained by using partial least squares-discriminant analysis and a fuzzy rule-building expert system. Relatively poor accuracy was obtained using soft independent modeling of class analogy when a single component was used.