The taxonomy of the Scutellaria pekinensis complex has been ambiguous and problematic, because morphological characters are variable. To elucidate the taxonomic structure of the Korean taxa belonging to the complex, 29 characters were measured from 99 individuals collected from 96 localities and analyzed by factor analysis, cluster analysis, and discriminant analysis. The results supported the recognition of four infraspecific taxa of S. pekinensis Maxim. in Korea: var. ussuriensis (Regel) Handel-Mazzetti, var. alpina (Nakai) Hara, var. transitra (Makino) Hara, and var. maxima S. Kim et S. Lee. Key characters distinguishing the four varieties were inferred on the basis of multivariante analyses.