The mechanical properties such as compressive strength and nanohardness were investigated for Pinctada margaritifera mollusk shells. The compressive strength was evaluated through a uniaxial static compression test performed along the load directions parallel and perpendicular to the shell axis, respectively, while the hardness and Young modulus were measured using nanoindentation. In order to observe the crack propagation, for the first time for such material, the in-situ X-ray microscopy (nano-XCT) imaging (together with 3D reconstruction based on the acquired images) during the indentation tests was performed. The results were compared with these obtained during the micro-indentation test done with the help of conventional Vickers indenter and subsequent scanning electron microscopy observations. The results revealed that the cracks formed during the indentation start to propagate in the calcite prism until they reach a ductile organic matrix where most of them are stopped. The obtained results confirm a strong anisotropy of both crack propagation and the mechanical strength caused by the formation of the prismatic structure in the outer layer of P. margaritifera shell.