Decline in population size may lead to decrease in genetic diversity, increase in inbreeding rate and also decrease in adaptation ability of populations against environmental changes. Therefore, monitoring genetic indices is one of the main tools for understanding the stable situation of species. In this study, the genetic diversity and population structure of the Goitered gazelle (Gazella subgutturosa) in Fars province (Bamou National Park and Basiran No-Hunting Area) were evaluated using 45 scat samples and 15 microsatellites. Indices of genetic variation, inbreeding, structuring, and bottleneck were estimated. Baesed on the results, the observed heterozygosity ranged from 0.34 to 0.95, indicating a relatively high level of genetic diversity in both populations. Additionally, the genetic differentiation index (FST) was estimated at 0.056, revealing a significant level of genetic differentiation between the two regions. This pattern may be resulted from gene flow limitation, geographic distance, and landscape resistance. There was no sign of bottleneck in the populations. Although moderate genetic variation was found, the presence of genetic structuring highlights the importance of improving habitat connectivity and considering the concept of management units in future efforts. These results can provide scientific bases for making conservation strategies and sustainable management of Iranian Goitered gazelles.