Pearl is the most valuable form of gem made by organisms and its beauty has been considered attractive and precious by people all over the world. Pearl oyster aquaculture system, in which a graft from the mantle pallium is transplanted with a nucleus into mother pearl oysters, is currently conducted at the industrial level. However, it is unclear what molecular mechanisms are involved in this system of pearl formation, which produces brilliant and beautiful nacreous layers. Since it takes long time to look for the proteins and genes possibly participating in the molluskan shell formation, another sophisticated strategy has been expected to screen candidate genes. One breakthrough in the latter area was the development of next-generation sequencing (NGS) in place of the automated Sanger method, the first generation sequencing technique. Using NGS, expressed sequence tag (EST) libraries were constructed from pallial mantle and pearl sac, which form the nacreous layer, and from the mantle edge, which forms the prismatic layer in the Akoya pearl oyster Pinctada fucata. Subsequently, the total genome sequence of the Akoya pearl oyster was analyzed. This database, together with the EST database mentioned above, is useful for identifying genes responsible for superior phenotype characters for pearl oyster aquaculture such as fast growth, disease resistance, easy domestication, and ability to produce high quality pearls. Subsequent marker-assisted breeding of the Akoya pearl oyster should establish strains with superior genotypes, producing even higher quality Akoya pearls.