The local deformation surrounding an indented area of Ensis siliqua mollusk shell is characterized using a Raman spectroscopic technique, the findings of which are related to the material’s mechanical function. Microhardness indentation of four directional planes is used to show the marked anisotropy of the structure, where the outer and inner layers of the shell are found to have a significantly higher microhardness value of 4.82 ± 0.02 GPa, compared with transverse and longitudinal cross-sectional values of 3.00 ± 0.07 GPa. This difference is related to the crossed lamellar microstructure of the shell, which is oriented to provide the maximum resistance to external attack from predators. Nanoindentation of the material shows no such anisotropy, giving mean hardness and modulus values for the four directional planes of 3.86 ± 0.10 GPa and 82.4 ± 2.7 GPa respectively, thereby clarifying the prominent role of microstructure in such materials. Scanning electron microscopy of indented samples shows that plastic deformation and delamination occur to different extents, depending on the orientation of the structure and local microstructural features such as prismatic layers. A Raman spectroscopic technique has been used to map relative deformation in the vicinity of the indents, showing that the amount of plastic or permanent deformation can be quantified, and that material delamination can be distinguished from other forms of deformation such as local cracking. These experimental methods are repeated using samples of non-biogenic aragonite, which act as an analogous material for comparison with the shell. It is proposed that the analysis of microhardness indents using Raman spectroscopy could be applied to other biomaterials exhibiting anisotropy.