Since the foundation of the INPA and the enforcement of the wildlife protection laws, the wild population of the Nubian Ibex (Capra nubiana) has grown to an estimated size of 1000 individuals. The population’s natural distribution is dictated by an un-continuous landscape of cliffs and water sources in the Judean and the Negev desert, while Human development leading to landscape fragmentation can further limit wild ungulates movement. The only study that dealt with the population level was based on the INPA rangers’ opportunistic sightings, thus its conclusions are limited and gene flow isn’t evidential. We intend to use genetic methods in order to better describe the population genetic structure and to assess the connectivity between sub-populations. We further want to test whether the habituation process taking place can promote a fine-scale genetic structure through behavioral changes that affects both group structure and dispersal. A better understanding of the spatial-behavioral and genetic dynamics of the Ibex can help its protection and serve to design a long term management program, enabling conservation efforts to focus their attention to where it is most needed.