Scaphopod molluscs are marine, infaunal, cosmopolitan animals. They encase their soft tissue with an aragonitic tusk-shaped shell that has at its two ends an orifice, the aperture and the apex. We investigated the shell of the dentaliid species Fissidentalium metivieri and Antalis weinkauffi and characterized shell crystal organization with electron backscatter diffraction (EBSD) and laser confocal and scanning electron microscopies. Based on crystal size, morphology, organization and growth-line spacing, we distinguish five different crystal arrangement motifs in the investigated shells. We find two slightly different microstructures for the shell proper, two microstructures for the attachment of muscles to the shell and one microstructure for a secondary hard tissue growth product, secreted at the apical orifice. Crystal organization motifs are crossed-lamellar, dendritic and prismatic. Crystal textures are crossed-lamellar, axial-like and crossed-lamellar-like. Crystal organization with a crossed arrangement is utilized for shell formation by representatives of many Ca-carbonate shell-secreting mollusc classes/subclasses: Scaphopoda, Gastropoda, Bivalvia, Polyplacophora (crossed-lamellar), and Patellogastropoda (crossed-foliated). Based on structural–crystallographic attributes, we highlight a basic shell structure that is broadly similar for the species of these mollusc classes/subclasses. However, this basic crystal arrangement motif is significantly modulated by the specific crystal organization that is inherent for a particular mollusc class/subclass.