Abstract: In order to research the relationship between syntaxin17(STX17) gene and Mongolian horse coat color and mechanism, the polymorphism in intron 6 and the relative expression quantity in different colors skin of Mongolian horse were analyzed by seminested PCR and realtime quantitative PCR. The results showed that 4.6 kb duplication segments existed in intron 6 of STX17 gene in gray Mongolian horse, but not existed in nongray Mongolian horse by seminested PCR. The expression level of STX17 gene was highest in gray skin and lowest in bay skin by realtime quantitative PCR. The results indicate that the STX17 gene has typical relationship with gray Mongolian horse.