Breeding ornamental white sika deer is a new notion that can be used to broaden the sika deer industry However, it is very rare for other coat phenotypes to occur, especially white (apart from albinism), due to the genetic stability and homogeneity of its coat color phenotype, making it difficult to breed white sika deer between species. We found a white sika deer and sequenced its whole genome. Then, the clean data obtained were analyzed on the basis of gene frequency, and a cluster of coat color candidate genes containing 92 coat color genes, one SV (structure variation), and five nonsynonymous SNPs (single nucleotide polymorphisms) was located. We also discovered a lack of melanocytes in the skin tissue of the white sika deer through histological examination, initially proving that the white phenotype of sika deer is caused by a 10.099 kb fragment deletion of theSCFgene(stem cell factor). By designing SCF-specific primers to detect genotypes of family members of the white sika deer, and then combining them with their phenotypes, we found that the genotype of the white sika deer is SCF789/SCF789, whereas that of individuals with white patches on their faces is SCF789/SCF1–9. All these results showed that theSCFgene plays an important role in the development of melanocytes in sika deer and is responsible for the appearance of the white coat color. This study reveals the genetic mechanism of the white coat color in sika deer and supplies data as a reference for breeding white ornamental sika deer.