Silicon is by far the most abundant element in the earth crust and also is an essential element for higher plants, yet its biology and mechanisms in plant tolerance of biotic and abiotic stresses are poorly understood. Based on the molecular mechanisms of the biosilicification in marine organisms such as diatoms and sponges, the cell wall template-mediated self-assembly of nanostructured silica in marine organisms and higher plants as well as the related organic molecules are discussed. Understanding of the templating and structure-directed effects of silicon-processing organic molecules not only offers the clue for synthesizing silicon-based materials, but also helps to recognize the anomaly of silicon in plant biology.