Abstract: In order to explain the reason of coat color separation in the F1 hybrid of Duroc × Luchuan Pig populations，five litters of piglets with black coat color and the sows were studied as controls，by sequencing of PCR products，we analysed the genotype of MC1R gene in four litters of piglets with coat color separation and the sows. Sequencing results indicated that the MC1R genotype in piglets of control samples was ED1/e，and in the sows was ED1/ ED1；among the four litters of piglets with coat color separation and the sows，the MC1R genotype of black piglets， red piglets and the sows were ED1/e，e/e，ED1/e，respectively. The MC1R genotype in purebred Duroc is e/e and the purebred Luchuan pig is ED1/ ED1，the F1 hybrid should be ED1/e. So the results confirmed that the sows farrowing red piglets were heterozygous and infiltrated by Duroc descent. From this study，we revealed the reason for coat color separation of Duroc × Luchuan Pig populations from the molecular level. According to the coat color of piglets，we can quickly eliminate the heterozygous Luchuan sows.