Abstract: This experiment was conducted to study PAX3 expression and location in alpaca skin. In the study, the distribution of PAX3 protein was studied by immunohistochemistry，the expression level was analyzed by ImagePro Plus software and Western blot. The result showed PAX3 protein was mainly located in melancytes during the basal cells of hair bulb, around dermis papilla and in hair root. By ImagePro Plus software and Western blot analysis, the protein expression level was significantly different in different coat color (P<0.05). Based on the result, it indicates that PAX3 plays an important role in the melanocytes proliferation, differentiation and pigmentation.