The long-tailed goral (Naemorhedus caudatus) is classified as an endangered species in South Korea due to population declines driven by human development and habitat fragmentation. This study aimed to investigate genetic characteristics and microsatellite genotypes in long-tailed goral populations using fecal samples collected from Uljin and Samcheok regions, which are geographically important habitats for the distribution and dispersal of this species in South Korea. The mean expected heterozygosity (HE) and observed heterozygosity (HO) across 10 microsatellite loci were 0.600 and 0.461 for the Uljin population and 0.644 and 0.571 for the Samcheok population, respectively. These values indicate a moderate level of genetic diversity compared to other closely related species. Genetic differentiation between the two populations had a low level, while a moderate gene flow was observed. The genetic evidence obtained in this study suggests that these two populations share a similar genetic pool, resulting in a low level of genetic differentiation between them. Therefore, they should be considered as one continuous population. Results of this study provide fundamental data and valuable genetic insights for long-term management of the long-tailed goral population in Uljin and Samcheok regions.