Pinctada fucata martensii is an ideal animal for study of biomineralization. Although dozens of genes have been identified, the molecular mechanism of biomineralization remains still unclear. The purpose here was to discover the expression profiles of nine biomineralization genes in related tissues: mantle edge (ME), mantle centre (MC) and pearl sac (PS), and to explore the relationships between expression level and nacre thickness. The expression levels of seven genes (ACCBP, aspein, CaM, EFCBP, KRMP, nacrein and prismalin‐14) showed no significant difference between ME and MC, but were significantly higher than those in PS. The expression level of N19 was the same in ME and PS, significantly higher than that in MC. However, msi60 in ME, MC and PS showed no significant differences in expression level. In addition, the correlations of expression levels between ME, MC and PS were highly significant, indicating that there are some similar function and mechanism among the three tissues. Also the nine genes had significant correlation of expression levels between one another. Furthermore, no other genes from oysters which produced pearls of different grades showed significant difference in the expression level, except CaM in MC, which had significantly higher expression level in the medium pearl grade than in the plain nucleus grade. Moreover, the expression level of msi60 in MC of host oyster was significantly correlated with produced pearl layer thickness, suggesting that msi60 might play an important role in pearl formation and host oyster may also participate in the development of pearl.