Mongooses are carnivore species of which two species, Indian grey mongoose (H. edwardsii ) and small Indian mongoose (H. auropunctatus ), have been identified in Iran. These two species are distributed in the southern part of Iran from Sistan and Baluchistan province in eastern Iran to Ilam province in the west. In this study, genetic diversity of the Indian grey mongoose was investigated. In this study,24 samples of H. edwardsii and three samples of H. auropunctatus were collected across the southern part of the country. A fragment of 527 bp of Control region was amplified and sequenced. Results of genetic diversity showed high haplotype (0.891) and nucleotide (0.0427) diversities. Analysis of molecular variance showed that the majority of the genetic variance was distributed within populations (68.48) and 32% was among populations. The fixation index (F ST ) was estimated at about 0.31. The results of phylogenetic analysis showed that the Indian grey mongoose in Iran has divided into two distinct clades, distributed in the west and the central part of Iran, of which the western clade showed higher haplotype diversity. All of the small Indian mongoose sequences obtained in Iran formed an identical haplotype and different from other small Indian mongoose haplotypes recorded in the GeneBank from other parts of the species range. In this study, habitat suitability modeling was performed and the effects of climate change on the Indian gray mongoose distribution was evaluated using MaxEnt model. Results showed that three variables, including distance from agricultural lands, urban areas and water resources had the greatest roles in the habitat suitability models of the Indian grey mongoose. In order to predict the effects of climate change on the distribution range of the Indian grey mongoose, two ecological models including MIROC5 and CCSM were used with two moderate and severe scenarios. In all models, the highest habitat suitability was observed in Fars province. The results of this study can be used in the conservation and management of the mongoose populations and for the introduction of mongooses into different regions. Further ecological and phylogenic research are recommended to clarify the ecological and phylogenic status of the small Indian mongooses in Iran. Keywords : biodiversity, phylogenetic analysis, climate change, haplotype network, control region, Habitat suitability.