Electron backscatter diffraction (EBSD) is used to determine the detailed crystallographic orientation of calcite crystals of craniid brachiopods in the context of shell ultrastructure. Sections of shells of two Recent species, Novocrania anomala and Novocrania huttoni, are analysed to provide 3D crystallographic patterns at high spatial resolution. The c-axis of semi-nacre calcite crystals is oriented parallel to the laminae that define the ultrastructure of the secondary layer. This orientation differs from that of rhynchonelliform calcitic brachiopods where the c-axis is perpendicular to the length of morphological fibres and to the shell exterior.