Abstract The bivalve Pinctada margaritifera exhibits three main transplant phenotypes derived from the donor (from which a mantle graft tissue, the saibo , is excised), the recipient (into which the saibo is implanted with a nucleus, leading to the formation of a pearl sac “chimera”) and the cultured pearls themselves. This first phenome study on the species derived from a large experimental graft. Transplant phenotype was assessed at three scales: 1) macro, pearl size, colour, grade, 2) micro, pearl surface microstructure, and 3) molecular, biomineralisation gene expression level in saibo and pearl sac tissues. From donor to pearl, the phenome revealed fine variations of quality traits dependent on the position on the mantle where the saibo was cut, whose variation could overlap with inter-individual donor phenotype differences. A single donor phenotype could therefore produce multiple pearl phenotypes at the scale of the saibo position, mirroring its original activity at the mantle position level and the colour and shape of the shell. This phenome study provides essential information on phenotypic trait architecture enabling us to explore and explain the main biological functions and pave the way for a phenomic project on P. margaritifera that could benefit the pearl industry.