The number of goitred gazelle populations had significantly decreased due to natural and anthropogenic threats over the last century. Today, the remaining populations of this species are confined to protected areas. Lack of detailed information about genetic variation, gene flow and phylogenetic relationships among populations of this threatened species has hampered conservation efforts. Landscape connectivity among the mainly isolated populations of goitered gazelle is required for reducing the effects of genetic threats. In this study, we examined factors that influence gene flow among six goitered gazelle populations in central Iran using a landscape genetic approach and non-invasive sampling method. In the first step, geographic distribution of goitered gazelle in Central Iran was predicted using 12 uncorrelated biogeographic variables. The distribution of potential habitats was strongly influenced by bioclimatic data, vegetation type and density and elevation. In the next step, genetic structure, gene flow and taxonomic status of goitred gazelle was surveyed using 15 microsatellites markers and 400 bp of cytochrome b. Low levels of haplotype diversity were seen in populations. A total of five cyt b haplotypes were identified from 170 gazelle samples. The microsatellite markers showed higher genetic variation than cyt b. The gazelles in the Mooteh and Biduyeh protected areas showed the highest and lowest genetic and haplotype diversity respectively. Individual-based bayesian clustering algorithms revealed three highly admixed genetic populations including: Biduyeh (first group), Kolah-Ghazi (second group), Mooteh, Ghamoshloo, Kahyaz and Kalmand (third group). The effect of natural and anthropogenic factors on observed genetic structure was elucidated using isolation index, isolation by distance (IBD) and isolation by resistance (IBR). IBD analysis showed a positive but insignificant correlation with geographic distance (R 2 = 0.30; P= 0,026). Isolation by resistance showed that IBR has greater impact on the gazelle population genetic structure than IBD (R2 = 0.4 2 ). Based on the obtained results, we concluded that a combination of geographic distance, landscape resistance and anthropogenic factors, influence genetic structure and gene flow in goitered gazelle populations in central Iran. The obtained results highlight the conservation importance of goitered gazelle populations in Biduyeh, Kahyaz and Kolah-, which should be considered as separate management units. The results of this study can be used in designing migration corridors. Keywords : Goitred gazelle, Gene flow, Microsatellite, Genetic structure, Cytochrome b, Landscape genetic, Central Iran.