Dried root of Codonopsis species (Campanulaceae), commonly known as "Dangshen" or "Dangshen Radix" is a multipurpose crude drug used in traditional Chinese medicinal system. The drug is sometimes used as a substitute of much expensive Panax ginseng. Due to variation in processing methods and producing areas, Dangshen is known by several trade names. This results in confusion of crude drug administration and application. Accounding to Chinese Pharmacopoeia, 3 species of Codonopsis; C. pilosula, C. modesta and C. tangshen have been mentioned as sources of the crude drug "Dangshen". In Taiwan, C. javanica, C. kawakamii and Campanumoea lancifolia known as "Tu-dangshen" are commonly used as "Dangshen Radix", Codonopsis kawakamii is indigenous to Taiwan. The morphological features of dried roots of these six plant species are quite similar; hence it is difficult to identify these species on the basis of physical appearance alone. In the present study, Internal Transcribed Spacers (ITS)-based analysis was used to ascertain the phylogenetic relationship among the six species. Results showed that the length of the ITS regions among the six species ranged from 638 to 655 bp and the contents of GC in ITS (ITS1+5.8S+ITS2) regions ranged from 60.31 to 62.52%. The lengths of ITS and GC contents of ITS sequence and molecular phylogenetic trees of six Dangshen sources indicate that C. javanica has more homology to Campanumoea lancifolia than the other four species of Codonopsis.