This study analyzed the relationship between the lunar phase and the reproductive cycle of Pinctada margaritifera inhabiting Weno Island, Chuuk Lagoon, Micronesia. We measured indicators of maturity (gonadosomatic index [GSI]and sexual maturation-related genes) and investigated changes in the gonadal maturity stages (GMS) of P. margaritifera over lunar cycle. GSI was higher around the full moon. GMS of P. margaritifera were classified as the early gametogenesis stage, ripe and spawning stage, and spent and degenerating stage. A large percentage of oysters was observed in the ripe and spawning stage at the first quarter moon in female and the full moon in male as well as in the spent and degenerating stages at the third quarter moon in both sexes. In addition, the expression of doublesex- and mab-3-related transcription factor 2 (DMRT2) in the male P. margaritifera black-lip pearl oyster was the highest during the full and third quarter moon phases, whereas no difference in expression was observed with the lunar phase in females. In contrast, the expression of vitellogenin (VTG) was the highest in female P. margaritifera during the first and third quarters. No difference in expression was observed according to the lunar phase in males. The results suggest that the lunar phase directly affects the expression of sexually mature gonads in P. margaritifera black-lip pearl oyster.