High resolution EBSD analysis was carried out under specific experimental conditions (15 to 5 kV) on the skeleton of the modern carbonate brachiopod Gryphus vitreus and resolved nano- to microscale preferred crystallographic orientation patterns undetcted so far. As biologic superstructures are formed by controlled nanoparticle assembly it is essential to resolve their internal structure and texture with the highest possible spatial resolution. Low kV EBSD (15 kV and at 5 kV) provides the required resolution. We observe in the investigated carbonate skeletons a strongly interlocking microstructure of concave/convex grains. The interface topology of the interdigitating structure reaches below the micrometer scale. Individual grains reach sizes up to 20 µm (or even more) in one dimension. They show a mosaic spread of several degrees such that they must be addressed as mesocrystals. Even though the shell consists of three different microstructures with completely different crystal morphologies and grain boundary topologies the crystallographic texture of the three layers is similar. This indicates that distinct control mechanisms prevail when the shell is formed.