Abstract: In order to explain the reason of coat color separation in thehybrid of Duroc and Baoshan pig and seek molecular marker to determine the purity of Baoshan pig. PCR amplification, molecular cloning and multiple sequence alignment techniques were used to analyze MC1 R gene CDS in Baoshan pig and MC1 R genotype in its hybrid piglets（S1-S6 litters）.The results showed that the MC1 R gene CDS of Baoshan pig was 963 bp in length, encoding 321 amino acids. Compared with wild boar, Baoshan pig had five SNPs in the coding region of MC1 R gene. Two missense mutations and three synonymous mutations occur at the translation level. The two missense mutations were the 283 st（G＞A）, the 305 st（T＞C）, and the three synonymous mutations were the 51 st（G＞A）, the 363 st（T＞C）, the 729 st（G＞A） bases. This indicated that the allele regulating the black hair color of Baoshan pig was E^D1. The S1～S4 litters of piglets were the purebred Du x Bao pigs, and they were all black, which had three SNPs at base 491 C＞T,727 G＞A and 729 C＞A, and the DNA profiles showed that this three SNPs are all double peaks, whose genotype was E^D1/e. The S5 litter of piglets were the hybrid Du x Bao pigs, and their offspring appeared black piglets and yellow piglets. The genotype of black piglets and yellow piglets were E^D1/e, e/e. The S6 litter of piglets were hybrid Du x Bao pigs, and their offspring appeared black piglets and black-yellow striped piglets and the genotype was E^D1/e. It is suggested that MC1 R gene can be used as a molecular marker to explain the color separation of Baoshan pig and determine whether it is a pure breed or not.