The Pacific oyster Crassostrea gigas is cultured worldwide due to the advantages of rapid growth and good adaptability, and has become one of the most commercially important bivalve species. In our successively selective breeding, three strains of C. gigas with black, white and gold shell color traits have been developed. Tyrosinase (Tyr) is known as one of the most important enzymes in the regulation and production of melanin in animals. In this study, exons in the C. gigas TYR gene (CgTyr1) were sequenced. Mutations of the CgTyr1 gene and its association with shell color were analyzed in the three shell color strains of C. gigas. A total of 23 single nucleotide polymorphisms (SNP) were detected using single-strand conformation polymorphism (SSCP) and sequencing analysis, of which 11 SNP loci had highly significant differences between the three shell-color strains. In the SNP loci with significant difference, mutation c.591C/T, c.632G/A and c.1155T/C are non-synonymous which lead to amino acid changes Ala122Val, Gly136Ser and Phe310Ser. For further analysis, 11 SNP loci with a highly significant difference were selected for haplotype construction. One specific haplotype for every shell color strain was constructed and confirmed in the validating group. The mutations and haplotypes that are strongly associated with the shell color phenotypes in this study could be useful in understanding the molecular mechanism of pigmentation, and could also be potentially applied to marker-assisted selection breeding programs for C. gigas.