Based on the investigations of crystal structure of nacre using SEM, TEM and XRD, it is proposed that there exists a domain structure of crystal orientation in the nacre. The orientation domain consists of continuous 3-10 tablets along the direction perpendicular to nacreous plane, and 1-5 tablets in a single lamina. The tablets in a domain are crystallographic identical in three dimensions. From the crack morphologies, it is found that the crack deflection, fibre pull-out and organic matrix bridging are the three main toughening mechanisms acting on nacre. The organic matrix plays an important role in the toughening of this biological composite. The biomimetically synthesized composite made of alumina and kevlar showed significant increase in the fracture energy compared with the single ceramics. The soluble proteins extracted from nacre can induce aragonite and the one from prism can induce calcite grown with the preferred orientation of 104. The insoluble proteins control the nucleation site and thus lead to a finer crystallization of CaCO3.