Mineralization in pearls is used as a ‘study model’ to understand basic mechanisms of calcium carbonate biomineralization. In addition to nacre formation, vaterite and calcite can be found in pearls, with the occurrence of calcite being the least studied. In this study, two calcite microstructures, prisms and “pseudo-prisms”, are described. Electron backscatter diffraction (EBSD) analyses show that there is no unique crystallographic orientation for a single calcite microstructure and, instead, each is composed of microcrystals with different orientations. Furthermore, general crystallographic orientations are found for prisms, with c-axis parallel to the long axis, and “pseudo-prisms” with the c-axis perpendicular to their elongation. Pseudo-prisms tend to be grouped in crystallographic domains. Overall, the formation of calcite structures in pearls may not be compared to biomineral structures in shells, which are better defined in terms of crystal habit and present a more constrained crystallographic control, in addition to having a strong correlation between crystallization and the formation of organic envelopes.