Biogenic silica is the major source of silica for diagenesis. One of the prominent examples is the presence of silica in phytoliths in the leaves of plants, ie. grasses, and Equisetaceae. Some suggested that silica present in phytoliths can serve as a defense mechanism against the herbivores, where the presence of silica in leaves increases the difficulty in digestion, harming the fitness of herbivores. However, evidence on the effects of silica on the wellbeing of animals and plants is still insufficient.  
Besides, sponges are another biogenic source of naturally occurring silica in animals. They belong to the phylum Porifera in the classification system. Silicious sponges are commonly found with silicified sedimentary layers, for example in the Yanjiahe Formation in South China. Some of them occur as sponge spicules and are associated with microcrystalline quartz or other carbonates after silicification. It could also be the main source of precipitative beds such as cherts beds or cherts in petrified woods.  
Diatoms, an important group of microalgae living in marine environments, contribute significantly to the source of diagenetic silica. They have cell walls made of silica, also known as diatom frustules. In some silicified sedimentary rocks, fossils of diatoms are unearthed. This suggests that diatoms frustules were sources of silica for silicification. Some examples are silicified limestones of Miocene Astoria Formation in Washington, silicified ignimbrite in El Tatio Geyser Field in Chile, and Tertiary siliceous sedimentary rocks in western pacific deep sea drills. The presence of biogenic silica in various species creates a large-scale marine silica cycle that circulates silica through the ocean. Silica content is therefore high in active silica upwelling areas in the deep-marine sediments. Besides, carbonate shells that deposited in shallow marine environments enrich silica contents at continental shelf areas.