Amorphous silica is the second most abundant biomineral on Earth, and is mainly produced by diatoms, a large class of unicellular, eukaryotic algae. Diatoms are able to build up an enormous variety of genetically controlled threedimensional (3-D) silica shapes and nanopatterns. Studying the molecular mechanism of diatom silica morphogenesis will not only provide important clues to the mechanism of biological silica formation, but is also expected to lead to novel, environmentally benign pathways for the production of silica-based nanomaterials with controlled 3-D architectures. The recent determination of the genome sequence of the diatom Thalassiosira pseudonana, the establishment of methods for its molecular genetic manipulation, and the identification of T. pseudonana biomolecules involved in silica formation, have established this organism as the model system for silica biomineralization research. In this chapter we will summarize these new data and evaluate their significance for understanding the molecular mechanism of diatom silica morphogenesis.