Closely related mineral-producing organisms share common biomineralisation processes. We demonstrate that, in cases of disparate mineral structures where crystal growth mechanisms are necessarily diverse, nucleation processes are the common underlying mechanism during shell formation. Detailed crystallography in the context of shell microstructure in two morphologically distinct calcite brachiopods indicates that, despite differences in shell growth and fabric, at the centre of growth, calcite crystals nucleate with the c-axis 0001 parallel to the shell surface. Such detailed contextual crystallography of biomineralisation using electron backscatter diffraction (EBSD) will have significant applications for future research in biological and medical sciences.