© 2022, Department of Environmental Sciences, Arak University. All rights reserved.Asia Minor Spiny Mouse (Acomys Cilicicus) is one of the endemic spiny mouse species of Turkey. The species is vulnerable to environmental threats as conservation measures have not yet been determined. Understanding the genetic makeup of the species and its responses to ecological factors is, therefore, an important issue to develop applicable conservation measures. In the study, we aimed to identify the Acomys cilicicus' haplotype diversity for Cytochrome b (CYTB), Growth hormone receptor (GHR), and Recombination activating gene 2 (RAG2) genes and to explore spatial relationships between environmental factors and haplotype diversity of each gene. The spatial distribution pattern of haplotype diversity of genes was estimated using the Geographically weighted regression (GWR) model and Inverse Distance Weighted (IDW) interpolation, respectively. Moreover, the Monte Carlo permutation test was applied to reveal the relationship pattern between environmental predictors and haplotype diversity through local coefficient estimates. As a result, a logistic prediction map of the GWR model was obtained to indicate the distribution of haplotype diversity of genes. Outputs also showed considerable spatial variability in local coefficients estimates with the negative or positive association, and it was understood that the distribution pattern of haplotype diversity is delineated accordingly. In that context, it was concluded that local fluctuations of environmental conditions might negatively affect the haplotype diversity of genes, thus decreasing the species' adaptability to environmental changes. Outputs of the study are valuable to support the conservation efforts of the target species and can be a guide for species with similar characteristics.