The interactions between species and their environments can shape the distribution of spatial genetic variations. Evaluation of niche overlap and environmental dissimilarity provides valuable opportunities to investigate how niche differences contribute to genetic divergence between populations that differ in their geographical distributions and environmental conditions. Nowadays, the formerly large continuous populations of Goitered gazelle in Iran have been confined to fragmented habitats due to natural and anthropogenic factors. A statistical framework based on an ecological niche modeling at the genetical management units (MUs) level was used to compare environmental niches and evaluate the effect of niche differentiation on genetic patterns of two management units of Goitered gazelle in Central Iran. We found low values of niche overlap between the management units. The niche equivalency hypothesis revealed that the niche of MUs is more significantly distinct than expected by chance. Also, the niche similarity test for both comparisons falls within the 95% confidence limits of the null distribution. These findings demonstrate that the niche of two MUs is rarely identical, but they tend to be more similar than expected based on random predictions and environmental background, which they occur. We concluded that, besides landscape resistance and geographic distance, ecological niche isolation is another factor affecting the genetic structure of gazelle populations in Iran. Conservation planning of this vulnerable species should focus on isolated populations as separate management units and landscape linkages to maintain gene flow between the genetically similar populations.