Populus euphratica Oliv. (Euphrates poplar) is one of the naturally distributed poplar species and limited to south and southwestern Turkey. The species possesses great importance for both renewable energy resources and persistence of a healthy river ecosystem. Due to increased habitat destructions and fragmentation by human activities, the distribution area of this species has become narrower. Hence, searching for potential genetic diversity present in species' genetic resources is of great importance in terms of its resilience to changing environment as well as breeding and use. To explore genetic structure and diversity of Euphrates poplar, natural populations in the GOksu and Euphrates river ecosystems were studied with 21 microsatellite DNA loci. Results demonstrated reduced level of genetic diversity (Ho:0.44, uHe:0.45) and low differentiation among two river populations (F-ST = 0.07), suggesting a common origin. It appears that severe past reductions in population sizes have resulted in loss of genetic variation in the species. Native populations of this species in two rivers seemed to be marginal with continued gene pool shrinkage. Therefore, they are in great danger of collapsing, mainly because of continued habitat loss and fragmentation. Genetic data generated with the current study provide important information which could be useful for future restoration and conservation studies of the species.