Abstract:Filamentous fungi not only are pathogenic but also play a significant role in heterologous expressing enzymes, chemicals, and pharmaceuticals. Along with the implementation and promotion of Human Genome Project, life science has entered functional genomics era. Proteomics study is a type of functional genomics research in order to understand cellular process mechanism, protein functions and their interactions, which provides a vast potential for future production of industrial enzymes and recombinant pharmaceutical proteins by filamentous fungi. This review summarized the research contents and methods of proteomics study, and its applications in filamentous fungi including pathogenic, antibiotic producing and cellulase producing strains. Furthermore, future studies in transcriptomics, proteomics and metabolomics could offer a full scale of understanding the metabolic network and regulations in filamentous fungi.