Selected-area electron diffraction (SAED) was combined with high-resolution transmission and scanning electron microscopic analyses to determine the crystallography of three nannoliths, Florisphaera profunda, Braarudosphaera bigelowii and Discoaster. F. profunda produces pentagonal-shaped plates whose [0001] direction (c-axis) is oriented parallel to its surface and in the elongation axis of the plate-like element. B. bigelowii produces thick, pentagonal plates, composed of five trapezoidal crystals with the c-axis oblique to the crystal plane. This species is characterised, crystallographically, by the development of cleavage faces, called "laminae". Conversely, Discoaster specimens are star-shaped calcite crystals that are composed of several bent, bar-shaped calcite elements, called rays. Based on SAED observations and calcite decoration experiments, Discoaster rays are single calcite crystals. The [0001] direction is likely perpendicular to the tangential plane of the central area, and each ray joins in the plane that is parallel to [0001]. The difference in the crystallographic nature between nannoliths and heterococcoliths suggests that the phylogenetic origin, and the evolutionary history, of nannolith-producing phytoplankton are completely different from those of heterococcolith-bearing coccolithophores.