Abstract: Genetic polymorphisms of milk epithelial mucin, MUC1, were assayed in five local goat breeds of Sichuan Province and Boer goat. Goat milk MUC1 exhibited rich genetic polymorphisms. A total of 22 genotypes and eight alleles of MUC1 were revealed in the goat breeds tested. Molecular weight of goat milk MUC1 was in the range of 205 ku to 278 ku, which were obviously higher than that of bovine. Alleles, genotypes and genotype distribution of MUC1 differed among the goat breeds. The gene heterozygosity and genetic variation of milk MUC1 was high in goats. Cluster analysis based on milk MUC1 polymorphism of the six goat breeds reflected their actual relationships.