Molluscs have a well-deserved reputation for being expert mineralizers of various shell types such as nacre. Nacre is defined as regularly arranged layers and stacks of approximately 0.5 microm thick aragonite platelets that are extracellularly formed within a complex mixture of organic matrix. The control of species-specific layer thickness by the animal is still enigmatic. Despite the recent findings on the periodic layer-by-layer structures of chitin layers and silk-like protein layers in nacre-type biominerals, little is known about how the interface is defined between two different layers. In this paper, we demonstrate the presence of covalently attached, hydrophobic amino acid side chains in the chitin matrix in the bivalve mollusc Mytilus galloprovincialis by the combination of infrared spectroscopy and mass spectroscopy. The accumulation of the modified chitin matrix at the interface is quantified by the critical aggregate concentration of the purified chitin matrix, which is approximately an order of magnitude smaller than that of pure chitin. Our finding suggests an active role of such chemically modified chito-oligosaccharides in the creation of a defined interface and guidance of the periodic matrix textures, which would result in unique material properties of natural mollusc shells.