Abstract: To study rDNA ITS sequence of Comus officinalis Sieb. Et. Zucc., and analyzed the rDNA ITS sequence of its different cultivated varieties. A pair of primers was selected by experi-ment. The ITS gene fragment was amplified using this pair of primers, and PCR products were purified with DNA gel extraction kit (AxyPrep~(TM)) and sequenced by the method of Sanger dideoxy. Then the ITS1-5. 8S-ITS2 sequences were analyzed by the software of DNAssist Ver-sion 2. 0. The ITS1-5. 8S-ITS2 sequences was found whole ITS sequence consisting of 682 bp, ITS1 253 bp,5.8S 156 bp and ITS2 273 bp. The 5.8S gene sequences of 7 fruit shapes show highly coincidence. The ITS1 and ITS2 gene sequences of cylinderic shape, long pear-shape, el-liptic shape and spindly shape are in coincidence. The short cylinderic shape have 1 variable site in 3’end of ITS1 and 5’end of ITS2. The short pear-shape have 3 variable site in 5’end of ITS1 and the long clinderic shape have 5 variable site in ITS1. The ITS1 and ITS2 gene fragments are conservative at specific level in C. Officinalis. While they are less difference among some culti-vars. So they can being molecular marker for authentication of C. Officinalis Sieb. Et. Zucc.