In French Polynesia, the aquaculture of Pinctada margaritifera (Linnaeus, 1758) covers a large maritime exploitation area, spread over nearly 20 degrees latitude and longitude, with numerous pearl farms located in three archipelagos (Gambier, Society, and Tuamotu). As these archipelagos have specific seasonal temperature patterns each year, pearl oysters are subject to disparate and contrasting environmental regimes. This study aimed to examine the specificity of commercial pearl quality traits (n = 2,236 samples) at the archipelago scale, in such a way as to provide preliminary data to design the most appropriate strategy for the distribution of hatchery-produced phenotypes. A large and standardized grafting experiment using the same donor phenotype was designed and carried out over six grow-out locations, covering the three archipelagos. Results revealed significant differences in commercial pearl quality traits among archipelagos, giving these groups of growing sites distinctive “signatures”: (1) more color, less circles, and higher overall pearl grade in Gambier; (2) larger size with paler pearls in Tuamotu; and (3) darker pearls with intermediate size in Society. Characteristic differences in the environment and seasonal temperature ranges among the three archipelagos, corresponding to their distinct environmental conditions, can explain the specific variations between pearl quality traits among the sites. The strong disparities at archipelago scale should be taken into account in selective breeding programs for P. margaritifera so as to choose the most appropriate pearl oyster donor phenotype for use in each environment and thus enhance site-specific qualities for pearl production.