Cenozoic silicoflagellate evolution led to ten known genera derived from two groups classified together in Corbisema that may have survived the end-Cretaceous extinction. These underwent rapid diversification and gave rise to at least five genera before the end of the Paleocene, including Dictyocha and Naviculopsis. Important silicoflagellate evolutionary events include the emergence of corner-aligned double skeleton configuration by the early Paleocene and the sinistral rotation of the Dictyocha byronalis apical bridge in early to middle Eocene that evolved into the apically-ringed silicoflagellate genera (e.g., Distephanopsis and Stephanocha). We interpret Paramesocena and Octactis as descended from Stephanocha, although their precise evolutionary paths remain uncertain. The earliest Octactis has thicker apical ring elements than modern O. pulchra, and is here described as the new species O. kosciuszkoi. New combinations are provided for Stephanocha antarctica and Dityocha octangulata.Overall, Cenozoic silicoflagellates show a trend towards more complicated apical geometries and smaller portals. These features enable silicoflagellate double skeletons to form near-spherical skeletal structures that support the external cell boundaries during mitosis. Silicoflagellates employ various strategies to hold double skeletons together and support the cell boundaries across the portal and window openings. Variability is an important feature of the silicoflagellate skeleton and occurs in two broadly different contexts. The first occurs for all silicoflagellate species, with occasional variant skeletal designs distinct from the predominant morphology. The second variability is associated with a single taxon, where multiple unusual skeletal shapes occur in a silicoflagellate plexus over a geologically narrow time interval and limited geographic extent.