Abstract: The genus Aspergilli is an important industrial workhorse with extensive application in variety of fermentation industrial process, like producing food ingredient, enzymic preparations and organic acid etc. With the development of the technologies, the exploitation of Aspergilli has attracted more attention and gradually been developed to be the multi-purpose of cell factories. The review will highlight most recent breakthroughs in fundamental and applied Aspergillus research with a focus on new molecular tools and products. Genomics, transcriptomics, proteomics and metabolomics of Aspergilli has been summarized. New trends and concepts related to Aspergillus as the cell factory will be discussed.