Higher fungi or called as macro-fungi, consisting of the divisions ascomycetes, basidiomycetes, and imperfect fungi, are receiving great interest around the world, because studies of higher fungi help us not only to find new edible and officinal resources but also to understand their complicated biology. In recent decades, a large number of useful substances from higher fungi have been isolated, identified, and characterized, which have important biological functions, such as reducing blood pressure, enhancing immunity, and possessing anti-cancer and anti-HIV and other pharmacological activities. This chapter will review the genetic manipulation tools for higher fungi, omics analysis of higher-fungus cell factories, and production of useful metabolites by higher fungi, including those of terpenoids, heterocyclics, polysaccharides, and polyketides. Trends in future development of cell factories of higher fungi for useful metabolite production will also be analyzed. Graphical Abstract Strategies for improving cell factories of higher fungi for useful metabolite production.