In order to understand the expression of MITF gene and its association with shell color in the Pacific oyster Crassostrea gigas, we verified the four MITF genes in oyster, analyzed the sequence and compared with multiple sequences of other species. And the transcriptome of each stage of oyster development was analyzed. We also studied the mRNA expression in different tissues and mantle of black shell and white shell oysters. We found that three of the four MITF genes were pseudogenes, which were confirmed by transcriptome and RT-PCR, and the only expressed MITF gene in oyster encodes 448 amino acids. MITF protein is a hydrophilic and unstable protein and contains a N-terminal domain (MITF_TFEB_C_3_N superfamily) and HLH domain which is a highly conserved functional domain. Transcriptome analysis found that MITF was expressed at various stages of ontogeny of C. gigas, and the expression reached the highest level at the juvenile stage. The results of mRNA expression in tissues showed that the expression level of MITF in mantle was significantly higher than those in other tissues. The expression level of MITF in the adductor muscle of oysters with black shell was significantly lower than that of oysters with white shell. However, the expression level in the mantle of oysters with black shell was higher than that of oysters with white shell, but not significant. Both in black and white shell oysters, the expression of MITF gene in the outer edge of the mantel is significantly higher than in the inner edge. The results show that MITF gene of C. gigas might participate in the regulation of the melanin’s formation and the development of oysters at the early stage of oyster shell formation, and it might also regulate tyrosinase Tyr2 gene of oyster and participate in the formation of melanin in mantle and shell. This study lays a foundation for further study on the formation mechanism of shell color in oysters.