Abstract：To study the identification and evaluation methods of Ultramicro Fructus Evodiae, samples of Ultramicro Fructus Evodiae were taken, respectively, from fifteen kinds of Evodia Rutaecarpa (Juss.) Benth., and its varietas, their total DNAs were extracted and cloned, and the ITS sequencee were determined by molecular biological techniques. The ITS1, 5.8S and ITS2 sequences of ultramicro Fructus evodiae from three plant species were obtained. The inner similitude of same species was above 98%, but the diversity among these sequences was about 27%. Analysis of ITS sequence fingerprint can provide an effective criterion for the identification of Ultramicro prepared herbs.