French Polynesia is renowned for the production of Tahitian black pearl. These gems are obtained by grafting a nucleus into the gonad of a receiving oyster together with a graft, i.e. a small section of mantle tissue of a donor oyster. This procedure initiates the formation of a pearl sack around the nucleus, and subsequently, the deposition of concentric layers of nacre. The nucleus plays a key-role in pearl formation and its characteristics influence markedly the quality of the final product. As it is manufactured from mollusc shells, it contains a small percentage of organics. In the present paper, we used a set of biochemical techniques to characterize and compare the organic matrices from two types of nuclei that are currently used in French Polynesia: that from the freshwater mussel Amblema sp., and that from the pearl oyster Pinctada sp. To this end, we extracted the matrices from nuclei and performed FT-IR, monodimensional electrophoresis, and enzyme-linked immuno-sorbent assay (ELISA). Our data show that the matrix associated with Amblema nuclei has a very different biochemical signature from that of Pinctada nuclei, a fact that may explain the improved tolerance of grafted oysters to nuclei of Pinctada origin. In the absence of complex physical methods of investigation, simple immunological techniques and FT-IR performed on the extracted organic matrix are extremely reliable and effective for discriminating nuclei from these two sources. We assert that such techniques can be used as a diagnostic test to track unambiguously the biological origin of nuclei to avoid fraud.