Non-invasive sampling methods, such as scat sampling, have facilitated genetic studies for conservation genetics researchers, however, the quality and quantity of extracted DNA have always been the main issues with these methods. In the current study, the genetic variation and population structure of wild sheep (Ovis gmelini) in Bamou National Park (Fars, Iran) were evaluated using the swabbing technique and eight microsatellites. The sampling method used showed high efficiency in genotyping individuals and can be considered for use with other species. Expected and observed heterozygosity ranged from 0.502 to 0.943 and 0.950 to 1.00, respectively, and the mean allele richness was 8.87, indicating considerable genetic variation in the population. In addition, inbreeding coefficient across all loci was 0.052. There was no evidence of a bottleneck in the population in the recent past. Despite the high level of genetic variation, the lack of gene flow between populations, and global threats such as climate change, highlight the necessity of implementing reintroduction programs to maintain the evolutionary potential of the species.