Hippophae rhamnoides ssp. sinensis is endemic to China, and it is a dioecious, outcrossing plant. Although many studies have been undertaken mainly on its agricultural, nutritional, medical, and ornamental value, little is known about its population genetics. This study uses random amplified polymorphic DNA to investigate the genetic diversity and population genetic structure of 13 natural populations of the subspecies sinensis. Fifteen primers amplified 107 reproducible bands, with 95 (88.79%) being polymorphic. The gene diversity within population was 0.168, considerably lower than that of tree species and most perennial, outcrossing species, but higher than that of annual or short-lived, selfing species. The Gst value showed that 18.3% of the total genetic variation resided among populations, a little lower than that of outcrossing species. The present results are quite similar to those previously reported in another subspecies, H ssp. . rhamnoides rhamnoides. The low genetic differentiation among populations in ssp. sinensis may be attributed to the long-distance dispersal of seeds facilitated by birds, in addition to its characteristics of outcrossing, wind pollination, and widespread distribution. No association between genetic distance and geographical distribution was found. The population relationships revealed by the UPGMA dendrogram parallel this result, in that genetic distance did not increase with geographic separation. This pattern of population differentiation may imply the adaptation of ssp. s populations to the local environment, given that its habitats vary greatly across its distribution.