Pinctada fucata mantle and pearl sac tissues were collected in September 2009 each from four individuals maintained at the Mikimoto pearl farm, Mie, Japan. Mantle pieces had been grafted to all individuals for pearling in April 2009. <p> Despite biological and economic importance, there is still far from comprehensive understanding of the molecular mechanisms underlying the shell formation in pearl oysters where two distinct calcium carbonate crystals, nacre and prism, are formed in highly controlled manners. In this study, we aimed to construct comprehensive expressed gene profiles in tissues responsible for the shell formation in the pearl oyster Pinctada fucata.