Mature individuals of the cinereous vulture, Aegypius monachus, number 15,600–21,000 birds worldwide and population size of the bird has been in decline due to poisoned baits and the decreasing availability of food. Approximately 12–16% of the global population of cinereous vultures spend their winters in Korean regions that are hence important areas. In this study, the population structure and genetic diversity of the cinereous vulture in South Korea were evaluated to clarify the relationships between the Mongolian and South Korean populations with genetic diversity assessed using mitochondrial DNA (mtDNA) and microsatellite markers. In the South Korean population, two unique haplotypes (Hap8 and Hap9) were newly discovered in their mtDNA, with three polymorphic sites and low-level genetic diversity. Most of the cinereous vultures in South Korea were represented by a single haplotype, Hap8, and analyses of phylogenetic trees and the haplotype network illustrated that Hap8 was clustered in Lineage D (Mongolia). Notably, the other haplotype, Hap9, was only identified in one individual in South Korea with an unexpected clustering in Lineage C (Caucasus region, Armenia, Georgia, and Kazakhstan populations), which indicated that it might have been a vagrant bird. The microsatellite loci ( n = 21) isolated from South Korean cinereous vultures indicated comparatively lower genetic variation, with a K value of 1. These results indicate that the origin of the South Korean population is most likely from one source population of the Far Eastern cluster (Mongolian population), which was also supported by the outcome of mtDNA analysis. This study improves our understanding of the population structure and genetic diversity between the Mongolian and South Korean cinereous vulture populations.