Objectives : The original plant species of Schisandrae Fructus (O-mi-ja) is prescribed as Schisandra chinensis $B_{AILL.}$, in Korea, but S. chinensis $B_{AILL.}$ and S. sphenanthera $R_{EHD.}$ et $W_{ILS.}$ in China. Moreover, fruit of several other species in genus Schisandra also have been used as the same herbal medicines. To develop a reliable method for correct identification of Schisandrae Fructus and to evaluate the phylogenetic relationship of S. chinensis and its related species, we analyzed internal transcribed spacer (ITS) sequences of nuclear ribosomal DNA (nrDNA). Methods : Twenty-four plant samples of three Schisandra species and one Kadsura species, S. chinensis $B_{AILL.}$, S. spenanthera $R_{EHD.}$ et $W_{ILS.}$, S. nigra $M_{ax.}$ and Kadsura japonica $D_{UNAL}$ were collected from each different native habitate and farm in Korea and China. The nrDNA-ITS region of each samples were amplified using ITS1 and ITS4 primer and nucleotide sequences were determined after sub-cloning into the pGEM-Teasy vector. Authentic marker nucleotides were estimated by the analysis of ClastalW based on the entire nrDNA-ITS sequence. Results : In comparative analysis of the nrDNA-ITS sequences, we found specific nucleotide sequences including indels (insertions and deletions) and substitutions to distinguish C. chinensis, S. spenanthera, S. nigra, and K. japonica. These sequence differences at corresponding positions are avaliable nucleotide markers to determine the botanical origin of O-mi-ja. Moreover, we evaluated the phylogenetic relationship of four plant species by the analysis of nrDNA-ITS sequences. Conclusions : These marker nucleotides would be useful to identify the official herbal medicines by the providing of definitive information that can identify each plant species and distinguish it from unauthentic adulterants for O-mi-ja.