Abstract: With the acceleration of the international Hapmap project and the development of high-throughput genotyping platforms in recent years, SNPs has been widely applied in the genetic studies of complex disease. Because of the preponderant characteristics of large quantity, wide distribution, high density and low mutations, SNPs has been used in genome-wide linkage analysis and association studies, and provides potential ways in distinguishing the population variation and identifying the susceptibility genes, risky haplotype, targeted drug and individual treatment of complex skin disorders. Here, we present a review in the advance of SNP application in complex skin diseases.