Long-term survival of Goitered gazelles in central Iran has been threatened because of isolation of existing populations and genetic threats. Effective management of these small and isolated populations needs to evaluate landscape connectivity among core habitat patches. In the present study, resistance surfaces were mapped as a function of twelve uncorrelated variables using species distribution algorithms. Given the limited empirical data of Goitered gazelle dispersal distances, we assessed different dispersal ability scenarios. Extent of core habitats, fracture zones, and dispersal corridors were identified using resistance kernel approach. Our finding showed that while gazelle population in Biduiyeh Protected Area has been isolated, there is relatively high dispersal rate among populations of Goitered gazelle in Mooteh National Park, Ghamishloo National Park, Kahyaz Protected Area, Kalmand-Bahadoran Protected Area and Kolah-Qazi National Park. Given the effect of roads and metropolises, functional connectivity between Kolah-Qazi and other populations is not possible. Based on genetic relationships and landscape connectivity results, we concluded that gazelle populations in Central Iran can be grouped into three separated subpopulations including 1- Biduiyeh P.A., 2-Kolah-Qazi N.P., and 3- gazelles in other protected areas. The obtained results show that integrated conservation management at landscape level need to be considered in maintaining gene flow among isolated and fragmented habitats.