Background : ‘baek-chul’(White atractylodes rhizome) widely used in traditional herbal remedies in Asia. A. Japonica and A. Macrocephala are used as ‘baek-chul’ in Japanese Pharmacopoeia but only A. Macrocephala is used as ‘baek-chul’ in Chinese Pharmacopoeia. Based on morphologic observation A. japonica has small infloresence diameter, white flowers and gynodioecism, whereas A. macrocephala has large inflorescence diameter, red flowers ,monoecism and developed rhizomes. but The distinction of these isn't easy. SSRs are very useful molecular markers for species identification. In this study, genetic diversity and identification between A. Japonica and A. Macrocephala were confirmed by SSR marker. Methods and Results : DNAs were extracted from leaf tissue of A. Japonica, A. Macrocephala and A. Japonica × A. Macrocephala (Breeding varieties, ‘Dachul’) using DNeasy plant Mini Kit (Qiagen, Hilen, Germany). these plants cultivated from RDA(Eumseong) and used for PCR amplification. The relative concentration of the extracted DNA was estimated Nano Drop ND-1000 (NanoDrop Technologies, Wilmington, De, USA) And final DNA concentration was adjusted to 5.5ng/μL. In this study 8 primer pairs were tested on 4 A. Japonica, 4 A. Macrocephala, 2 ‘Dachul’. These primers showed high polymorphism among and within four populations of A. macrocephala.(Zheng et al.). We detected interspecific and intraspecific SSR polymorphism by 3 primer pairs. Conclusion : The results showed that these markers were found to be useful for diversity analysis as they distinguished among Atractylodes spp. and also A.Macrocephala. This work is intended to serve as the basis for the breeding of new varieties in white atractylodes rhizome.