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Microstructure studies of various classes of materials show the presence of a strictly defined order. The basic structural elements, crystallites of the same or different phases, strive to determine the state with the smallest free energy. This leads to a special mutual misorientation of the neighboring grains. In the frame of the research electron backscatter diffraction in scanning electron microscope was used to characterize the crystallographic relationships in calcitic prismatic lamellas forming the outside part of the shell of Pinctada margaritifera. Occurrence of boundaries with specific orientation relationship, preferred by a given material was confirmed.