The silicoflagellates are a class of enigmatic chrysophytes characterized by netlike skeletons composed of opaline silica. Other major groups of siliceous plankton—the diatoms and radiolarians—exhibit evidence of decreasing size or silicification over the Cenozoic. We investigated trends in the silicoflagellate fossil record by constructing a species-level database of diversity and morphological metrics. This new database reveals a proliferation of silicoflagellate species with spined skeletons along with an increase in the mean number of spines per species over the Cenozoic. Although there is little change in skeleton size or silicification among species with spines, those without spines are larger than species with spines and exhibit a decrease in size toward the present. Increased grazing pressure combined with declining surface silicate availability may have shifted the costs and benefits of silicification, causing divergent responses in skeletal morphology between these different morphological lineages of silicoflagellates over time. We postulate that diminishing Cenozoic surface silicic acid availability may have predisposed large spineless silicoflagellate species to extinction, whereas increased grazing pressure may have contributed to the extinction of all remaining spineless species within the edible size range of grazers.