The geographic distance might contribute to the genetic differentiation of populations on the landscape. Understanding the mechanism of the geographic range that affects gene flow and genetic structure is beneficial to maintain the genetic diversity. Here we investigated the landscape genetic structure of sixteen natural populations of apricot representing two natural distribution ranges of wild common apricots (P. armeniaca) and siberian apricots (P. sibirica) using 18 microsatellite markers. The siberian apricots, which were originated from the North and northeastern China, represented the richer genetic variation and diversity than that of siberian apricots. We found that P. sibirica populations in the Northeast and Northwest of China likely belonged to discrete genetic clusters, while the northwestern populations seemed isolated on the edge. We speculate that this pattern could be a result of the currently complex ecological environment associated with their wide habitats range from west to east in China. While, Central Asian P. armeniaca populations showed a highly admixed structure which was probably due to the recent introgression in a limited geographic distribution region. Meanwhile, we also implemented Isolate by distance (IBD) study on the relationship between both genetic differentiation and related geographic gradients pattern. Our results showed asignificant association between geographical distance and genetic distance among wild populations of Chinese P. sibirica but in Central Asian P. armeniaca. Therefore, our results suggested that the genetic structure associated with eco-geographic patterns could affect the genetic differentiation and diversity, which varied differently in case of different Armeniaca plants, which might have an implication for establishing a conservationstrategy maintaininggenetic diversityinthesespecies.