The　Qinling　mountainous　region　is　one　of　the　world＇s　biodiversity　hotspots　and　provides　refuges　for　many　endangered　endemic　animals.　The　golden　snub-nosed　monkeys　(Rhinopithecus　roxellana)　are　considered　as　a　flagship　species　in　this　area.　Here,　we　depicted　the　genetic　structure　and　evolutionary　history　via　microsatellite　markers　and　combination　with　the　ecological　niche　models　(ENMs)　to　elucidate　the　intraspecific　divergent　and　the　impacts　of　the　population　demography　on　our　focal　species.　Our　results　revealed　three　distinct　subpopulations　of　R.　roxellana　and　also　uncovered　asymmetric　historical　and　symmetric　contemporary　gene　flow　that　existed.　Our　evolutionary　dynamics　analyses　based　on　diyabc　suggested　that　the　intraspecific　divergence　accompanied　with　effective　population　sizes　changes.　The　ENM　result　implied　that　the　distribution　range　of　this　species　experienced　expansion　during　the　last　glacial　maximum　(LGM).　Our　results　highlighted　that　geological　factors　could　contribute　to　the　high　genetic　differentiation　within　the　R.　roxellana　in　the　Qinling　Mountains.　We　also　provided　a　new　insight　into　conservation　management　plans　with　endangered　species　in　this　region.