Filamentous fungus is one of the economically important fungi in the production of food, enzymes, organic acids and biocontrol agents. The growth and metabolism of filamentous fungi are strictly limited by the environmental conditions and their stress tolerance and adaptability to the multiple environments. The stress tolerance and adaptability of those fungi aredirectly regulated by the genes involved in stress response. In this paper, we reviewed the advances in the research on thegenes involved in stress responses and the applications in enhancing the ability to tolerate the environmental stresses. This review can provide the main impetus for improvement of filamentous fungi and a large-scale application in the future.