In this study, we developed 11 microsatellite markers specific to A. crataegi using NGS to investigate the genetic relationships of A. crataegi populations from South Korea to circumferential Asian countries (China, Russia, Mongolia, and Japan). Further, two mitochondrial DNA (mtDNA) gene segments (COI and CytB) were sequenced from the samples. The population- and individual-based Principal Coordinates and STRUCTURE analyses collectively suggested that the South Korean population of A. crataegi is most differentiated from the Japanese population, whereas it was closer to Mongolian and Chinese populations. These results collectively suggest that northern populations, in particular, Mongolian populations can be considered as the most genetically compatible one as donee population, when the reintroduction program is launched. †These authors contributed equally to this paper.