Abstract Biominerals have attracted multidiscipline interest (e.g. in material, medical and bio-geosciences) due to their unique organic–inorganic microtexture. In this work, electron backscatter diffraction (EBSD) and topological analysis of pole figures show that aragonite nacreous layers of Pinctada martensii (marine bivalve) shells have a mesocrystalline organization, which consists of at least a two-level domain structure. Primary domains are related by twin laws. The twinning between the primary domains is described as “mesotwinning.” Each domain is twinned by (110) planes. Secondary domains inside the primary domains are submicrometre units, ranging from several to hundreds of microns in dimension. The secondary domains are separated by low-angle grain boundaries. Angles between primary domains are ca. 63.5° or 52.5°; angles between secondary domains range from 5° to 12°. The twin relationship is quantified and twin boundary patterns are discussed.