In the last years, the field of mollusk biomineralization has known a tremendous mutation. The most recent advances deal with the nanostructure of shell biominerals, and with the identification of several shell matrix proteins: on one hand, the complex hierarchical organization of shell biominerals has been deciphered in few models, like nacre. On the other hand, although proteins represent a minor shell component, they are the major macromolecules that control biocrystal synthesis. Until recently, the paradigm was to consider that this control occurs by two antagonist mechanisms: crystal nucleation and growth inhibition. Emerging models try to translate a more complex reality, illustrated by the huge variety of shell proteins, characterized so far. The primary structure of many of them is composed of different functional domains, some of which exhibit enzymatic activity, while others may be involved in cell signalling. Many of them have unknown functions. Today, the shell matrix appears as a whole system, which regulates protein-mineral, protein-protein, and epithelium-mineral interactions. These aspects should be taken in account for the future models of shell formation.