Aspergillus niger FGSC A1279 (kusA- and pryG-) was derived from A. niger ATCC9029 by gene knockout.This study is to survey the secondary metabolism in Aspergillus niger FGSC A1279 through transcriptome sequencing, by comparing the transcriptional profile of two mutants whose laeA gene was deleted or overexpressed. The relevance between the identified active secondary metoblic pathways and the secondary metabolisms detected by mass spectrometry could provide effective clues to explore evaluable products for medicine and industry.