Abstract: Sea buckthorn (Hippophae rhamnoides L.) is a perennial dioecious shrub or tree whose juvenile period lasts from 3 to 5 years. Sea buckthorn grows in many European and Asian countries and is widely used in cosmetology, biotechnology, pharmacology, and agriculture. This crop is a source of valuable vitamins, minerals, carotenoids, and flavonoids. Its phenotypic description does not provide accurate characteristics of a taxon at the species, subspecies, variety, and population levels; therefore, one should use molecular analysis. For this study, a collection of sea buckthorn samples of different ecological and geographical origin, which consisted from herbarium samples and samples harvested in natural populations, was prepared. ISSR markers efficiently revealing genotypic difference between the samples were selected, and binary matrices were created for the further dendrogram construction. The performed analysis revealed a high level of intraspecific polymorphism and showed that samples of a similar ecological and geographical origin tended to group into clusters and were located at different genetic distance. The results of the study can be used to evaluate the diversity of forms of this crop, relations between them, their ecological and geographical origin, and the evolution of certain taxa. These results may also be used for a genetic passportization and identification of varieties prior to them reaching the generative period and for the pair selection for crossing. © 2020, Allerton Press, Inc.