Objective To research the cytological mechanism of the genesis of different coat color in alpaca by investigating the regulation mechanism of the SCF/c-KIT signal on the cell division, proliferation and distribution of alpaca hair follicle melanocytes. Methods We selected eight mature female alpacas, four with pigmented coat color and four with natural white coat color. Immunohistochemistry was used to identify the expression distribution of SCF and c-KIT receptor. Comparative quantitative RT-PCR was used to determine expression levels of SCF and c-KIT genes. Results The expression of SCF and c-KIT immunoactivity was detected in different coat color skin, but the expression level and localization were different in the hair follicle. ΔΔEM>Ct/EM> method was used for quantitative analysis of the expression levels of SCF and c-KIT genes in different coat colors of alpaca skin. The comparative expression of gene SCF in colored skins was 2.41 times of white skins, and the comparative expression of gene c-KIT in colored skins was 1.20 times of white skins. Conclusion SCF/c-KIT signal regulates the hair follicle melanocytes proliferation and division. The mature degree and mounts of melanocytes in hair follicle play central role in the genesis of coat color of alpaca. Furthermore, the differential distribution of melanocytes in hair follicle is mainly regulated by the