The crystallographic orientation and its relationship to the morphology of coccoliths were investigated for the Neogene-Quaternary calcareous nannoplankton Umbilicosphaera lineage using scanning electron microscopy (SEM) and electron back-scattered diffraction (EBSD). The c-axis of the calcite forming the distal shield elements was inclined upward at 66–68° (U. sibogae), 65–68° (U. foliosa), 57–58° (U. rotula), and 55–57° (U. patera) from the coccolith plane. Accordingly, the outward dip angle of one of the {101¯4} faces forming the surface of the distal shield of U. patera coccolith was shallower than those of U. sibogae and U. foliosa, explaining the nearly flat distal shield and the steep inner slope, formed by another equivalent {101¯4} face, around the central opening of U. patera. Our results showed that the evolution from U. rotula to U. patera during the Late Miocene was not accompanied by a change in crystallographic orientation. In contrast, the evolution from U. patera to U. sibogae and U. foliosa during the Pliocene was accompanied by a rotation of the orientation. The crystallographic orientation of calcite nuclei on the baseplate with a combination of other factors would have resulted in species-specific differences in shield shape and suture lines within the same phylogeny, consequently producing morphological diversity in the coccolith throughout geological time.