Sea buckthorn (Hippophae rhamnoides) is important environmentally and as a new commercial berry crop. Fourteen cultivars of sea buckthorn from China, Russia and Mongolia were evaluated for genetic relationships using RAPD data. Nine random primers were used to generate 114 RAPD markers by PCR. Among them, 103 (90.35%) were polymorphic. The genetic similarity ranged from 0.45 to 0.80 with a mean of 0.67. Genetic distance ranged from 0.23 to 0.80 with a mean of 0.40. Cluster analysis identified Zhongguoshaji from China (H. r. subsp. sienses) as the most genetically distinct cultivar. Hongguo (H. r. subsp. sienses), Zhongguoyou (H. r. subsp. sienses), the hybrid Liaohuerhao from China, Zeliang and Huoguang from Russia (H. r. subsp. mongolica) were clustered more distantly. The seven cultivars from Russia and Mongolia (H. r. subsp. mongolica) and the hybrid Liaohuyihao from China were grouped into two main clusters. Cluster I contained Chengsi, Liaohuyihao, Xiangyang, Chuyi andWulangemu. Cluster II consists of Nuyou, Hongyun and Aleiyi Data provide a scientific basis for selection and management of germplasm collections and crossing strategies for sea buckthorn.