Goat hair follicle stem cells were isolated by two different methods of explants culture and enzyme digestion. The resultant cells were cultured in vitro and identified by cell growth curve, immunohistochemical staining and colonyforming efficiency to compare the efficiency of the two methods for the cultivation and proliferation of hair follicle stem cells in vitro. The positive expression of K19 hair follicle stem cells in 1,3,7 passage recovered from explants were respectively 52.0%±1.62%,68.4%±1.82% and 72.0%±2.42%,the positive expression of integrin-β1 were respectively 52.5%±2.12%,66.3%±1.98% and 73.0%±2.16%,but the positive expression of K19 hair follicle stem cells in 1,3,7 passage from enzyme digestion were respectively 56.2%±3.12%,61.7%±1.17% and 64.0%±3.02%,that of integrinβ1 were 56.0%±112%, 63.0%±1.12% and 68.0%±2.32%. The CFEs of hair follicle stem cells in 1,3 and 7 passage by explants were respectively 18.4% ±0.77%,31.3%±0.88% and 44.7%±1.03%,but the CFEs of hair follicle stem cells in 1,3,7 passage by enzyme digestion were respectively 22.6%±230%,26.9%±0.86% and 32.8%±1.05%;The hair follicle stem cells isolated from explants could be subcultured for 19 passages in vitro but those from enzyme digestion could be passaged just 12 times in the same culture condition. The results showed that hair follicle stem cells can be separated by both methods and the stem cells from explants have higher efficiency in immunohistochemical staining, CFE and subculture ability than those from enzyme digestion when they were subcultured in vitro (P<0.01).