Habitat is one of the key parameters for species conservation, especially for endangered species . Having complete knowledge on the habitat requirements of a species is inevitable in order to develop management policies. With the proper parameters, managers can define suitable parts of the habitat which is most used by the species and improve their conditions. Habitat evaluation helps to analyse habitat changes over the time. Habitat modeling is a specific and reproducible method for describing, quantifying and mapping components of a habitat. In the current study habitat selection of Persian squirrel was evaluated in Dena, Eastern Dena, Khamin and Dil protected areas with ecological niche factor analysis (ENFA) and maximum entropy method (MAXENT). In the analyses, Slope, elevation, aspect, landuse, climate, vegetation type, distance from roads, distance from rivers and distant from villages were used as environmental variables. The results of ENFA indicated that climate, distance from rivers and aspect were the most important factors in habitat selection of Persian squirrel in Dena, Eastern Dena, Khamin and Dil protected areas. Favorable climate for Persian squirrel varied from Mediterranean to very wet climates. Persian squirrels prefer greater distances from rivers and western and southern aspects. Marginality and specialization factors were calculated at 0.531 and 2.94 respectively, which shows the Persian squirrel is a specialist species. The results showed that ENFA is not a suitable model for large- scale study of Persian squirrel habitat selection. The results of MAXENT indicated that landuse, climate and distant from road were the most important factors in habitat selection of Persian squirrel in Dena, Eastern Dena, Khamin and Dil protected areas. Persian squirrels prefer forested areas with very wet climate and areas near the roads. MAXENT was successful in implementing the model, with the mean AUC of 0.937. Overall, this study suggests that MAXENT is a more appropriate method for large-scale habitat suitability of Persian squirrel compared to ENFA. Keywords: Persian squirrel, habitat selection, habitat suitability, ecological niche factor analysis, maximum entropy