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Internal transcribed spacer (ITS), located between nuclear 18S and 28S ribosomal DNA genes, has been used for constructing phylogenic trees and determining taxonomic identity. In this work, ITS analysis was used for phylogenetic placements of Korean mugworts, Sajabal, Sajuari, and Injin, in relation to genus Artemisia. Direct sequencing of PCR products showed 642-3 bp of fully assembled ITS/5.8S region including 253-4 bp of ITS1, 167 bp of 5.8S rDNA, and 222 bp of ITS2. For a proper ITS analysis, the database of ambiguious sequences was modified either by making consensus sequence or by excluding the incomplete data. Although 5.8S rDNA was not informative site for taxonomic application within Artemisia due to high conservation, multiple alignment of ITS1 and ITS2 sequences indicated traditionally-named Sajuari mugwort to be A. verlotiorum.