Filamentous fungi are used by industry for manufacture of a large variety of useful products. The products include metabolites, enzymes and food. Fungal cells can grow at different environmental conditions and environmental diversity. The chemical and physical conditions used for fungal propagation which depends up on fungal genetics and biology will have a great impact on the capability of these cells to accumulate the desired product(s). Mevinolin, cyclosporine A, β-lactam antibiotics, pneumocandins, ergotamine, strobilurins, and mycophenolic acid are examples of revolutionary pharmaceuticals and agrochemicals that have a fungal origin in spite of the success of bioactive fungal metabolites as pharmaceuticals and agrochemicals and fungi remain s an essentially untapped source of medicines because only a small fraction of the vast fungal kingdom has been explored for bioactive metabolite production. However, recent advances in the genetics of microbial secondary metabolite biosynthesis, genomics, and metabolic engineering will play an ever-increasing role in facilitating fungal bioactive metabolites discovery.