Abstract: This experiment was conducted to explore the expression and localization of Wnt3a in different colors of alpaca skin. The tissues were obtained from white and brown adult alpacas skins. The comparative expression quantity of gene Wnt3a in different coat colors was analyzed by real time quantitative PCR. The protein expression and localization of Wnt3a were measured by Western blotting and immunohistochemistry. The results of QRTPCR showed that the comparative expression quantity of gene Wnt3a in brown alpacas was 2.970 2 times than that in white ones. The Western blotting results showed that the protein expression of wnt3a in brown alpaca skins was significantly higher than that in white alpaca. The positive signals of Wnt3a were found in hair bulb and outer root sheath of hair follicle, and the expression of Wnt3a was significantly different between the white and brown alpaca skin based on the average optical density (P<0.05). Our findings showed that Wnt3a may involved in the regulation of hair color formation.