Mollusc shells are organic–inorganic biocomposites, arranged in a limited number of superimposed calcified layers that generally exhibit very different organization of their crystallites. Because of their attractive mechanical and crystallographic properties, these shell layers have been the focus of several physical and biochemical characterizations. In particular, recent proteomic data obtained from individual layers suggest that their protein contents are different. However, the direct visual evidence that some macromolecular components are layer-specific is rather tenuous. This paper is based on a non-conventional immunogold labelling approach to localize proteins in the shell of the edible oyster Crassostrea gigas. The shell microstructure of this model organism is predominantly composed of foliated calcite, interspersed by discontinuous pockets of ‘chalky layers’, a porous microstructure typical of bivalves of the ostreid family. By developing a polyclonal antibody (in two rats) elicited against a proteinaceous shell fraction, we obtained differential staining of the two microstructures. We assert that our labelling is microstructure discriminant. The difference in labelling of the two shell microstructures suggests either that they are formed by a variation of the secretory repertoire of the shell-forming cells of the calcifying mantle epithelium or that the chalky layer may be formed via a completely different mechanism. Our results allow a first glimpse on the subtle regulatory mechanisms that drive the process of chalky and foliated layers deposition.