Abstract: In order to obtain the sequence of alpaca MC1R gene and explore the relationship between the expression level of MC1R gene and alpaca coat color, according to the sequence in GenBank （EU1358800）, a pair of specific primer was designed to amplify the cDNA sequence of MC1R using RTPCR technique. The MC1R gene sequence of white alpaca was cloned successfully and sequence analysis revealed that the MC1R gene, encoding 317 amino acids, was 1 081 bp in length. Compared with the published sequence in GenBank, the sequence identity was 99%. Also, 7 mutations were found within the gene. Further, a pair of primer was designed according to the sequence obtained. The relative expression level of MC1R gene in different coat color alpaca was analyzed using QRTPCR technique and SPSS 13.0 software. The relative gene expression level of MC1R in brown alpaca was 432 times than that in white alpaca after normalization with GAPDH gene（P＜001). It was indicated that the gene expression level of alpaca MC1R may be related to the coat color.