Publisher Summary Fermentation results from a variety of biological functions of microorganisms, including metabolism, biosynthesis, and reactions by secreted enzymes—some of which may be undesirable to accomplish high fermentation efficiency and obtain high quality of the product. Huge efforts have been made to improve the fermentation efficiency, by both the breeding of “A. oryzae” and modifying the fermentation conditions. The comprehensive genomic analyses will help to reconstruct biological systems including transcription networks and metabolic pathways in silica. A. oryzae is proven to be safe for human consumption, efficient in decomposing a variety of organic materials, and tolerant against extracellular conditions. The A. oryzae genomics project will lead to a new generation of fermentation processes, which can be used to increase energy efficiency in industrial processes and protect environmental conditions.