Biomineral forming organisms produce inorganic materials with complex, genetically encoded morphologies that are inaccessible by current synthetic chemistry. It is poorly understood which genes are involved in biomineral morphogenesis and how the encoded proteins guide this process. We addressed these questions using diatoms, which are paradigms for the self-assembly of hierarchically meso- and macroporous silica under mild reaction conditions. By isolating the intracellular organelle for silica biosynthesis, we identified a suite of new biomineralization proteins. Three of these, dAnk1-3, are specific to diatoms and contain a common protein-protein interaction domain indicating a role in coordinating assembly of the silica biomineralization machinery. Knocking out individual dank genes led to characteristic structural aberrations in silica biogenesis that point to a liquid-liquid phase separation process as underlying mechanism for pore pattern morphogenesis. Our work provides an unprecedented path for the synthesis of tailored meso- and macroporous silicas using Synthetic Biology.