The naviculopsid morphology, which consists of an arch across the minor axis of a basal ring with two corners and sides, is the simplest of the Cenozoic silicoflagellate skeletal designs that include an apical structure. This skeletal design is most often associated with the genus Naviculopsis (geologic range: middle Paleocene to early Miocene), but also occurs among other silicoflagellate genera. This paper interprets the evolutionary history for silicoflagellates of naviculopsid morphology, beginning with a group of large two-sided silicoflagellates from the late early Paleocene, recently placed in genus Pseudonaviculopsis, and ending with a late Miocene group of naviculopsid morphologies associated with Bachmnnocena diodon subsp. nodosa. Between these is Naviculopsis, which has more than twenty species recognized in deep sea sediments. A significant portion of the Naviculopsis taxa discussed in this paper are associated with plexus episodes of abundant and unusual variability from the late Paleocene, late Eocene and early Miocene. A possible explanation of the development of this skeletal morphology, as well as silicoflagellates with more complicated apical structures, is a need to decrease the size of portals, which may better support the cell boundary during mitosis.