Peroxisome (P), a ubiquitous organelle in the eukaryotic cells, is involved in various important metabolic processes. Investigation of formation, proliferation and degradation of the peroxisome is an important part of study of organelles biogenesis. So far, mechanism of the peroxisome biogenesis is not completely clear, although over 30 related genes were identified and characterized. Filamentous fungus, a multi-cellular eukaryotic organism containing many plant pathogens and economic species, holds great value of studying function and mechanism in the peroxisome biogenesis. The peroxisome researches have been progressed in recent years quickly after availability of the genome data and development of the fungal bio-techniques. Meanwhile greater interests have been demonstrated in area of the peroxisome biogenesis and in its roles of pathogenicity of several phytopathogenic fungi. The summary of mechanism of the peroxisome biogenesis in filamentous fungi and relationship between peroxisome and pathogenicity were reviewed in this paper