A total of 37 commercial samples of Fangchi Radix, including Sinomenium acutum, Stephania tetrandra, Aristolochia fangchi, and Cocculus orbiculatus, were collected from herb markets in Taiwan and China. The contents of 18 constituents in these samples were analyzed by high-performance liquid chromatography and were used to assess the potential relationships with their plant origins. A multivariate analysis, including a principal component analysis (PCA), cluster analysis (CA), and linear discriminant analysis (LDA) were used as the classification strategies. The successful natural groupings of the samples into 4 sets, namely, 5 S. acutum, 11 S. tetrandra, 15 A. fangchi, and 6 C. orbiculatus, were achieved by PCA and CA. The application of LDA gave the correct assignation percentages of 100.0% for all 4 groups.