The taxonomy of the Isodon excisus complex, which comprises I. inflexus var. inflexus, var. transiticus, var. macrophyllus, var. microphyllus, and var. canescens, has been ambiguous and problematic because their morphological characters are variable. To elucidate the taxonomic structure of the I. inflexus complex in Korea, 42 characters were measured from 70 OTUs representing the I. inflexus complex and were analyzed by a principle component analysis (PCA). The principle component axes 1, 2, and 3 (PC1, PC2, and PC3) represents 55.7% of the total variance. The characters showing high loading values for PC1, which have of absolute loading values higher than 0.7, were characters related to the leaf base and leaf teeth and the length of corolla tube. The length of the broadest part to the apex in the leaf, the density of non-glandular hairs on the lower surface of the leaf, and the length and width of the calyx were highly related to PC2 with the absolute loading values higher than 0.7. PC3 does not have any characters which have absolute loading values higher than 0.5. Three-dimensional scatter plots of the OTUs for the PC1, PC2, and PC3 axes showed that there are three taxa in the complex. Each area of I. inflexus var. inflexus, var. transiticus, and var. macrophyllus was completely overlapped, demonstrating that this taxon is I. inflexus var. inflexus. Areas for var. microphyllus and var. canescens were separated from that of var. inflexus in both cases. Therefore, we recognized three varieties, which are I. inflexus var. inflexus, var. microphyllus and var. canescens in the I. inflexus complex in Korea. This result also indicates that I. inflexus var. inflexus has a wide range of morphological variation. The recognition of var. microphyllus and var. canescens is also supported by the result of recent SEM studies of the fruit surfaces of Korean Isodon.