Biotransformation processes are defined as the use of complete biological systems or its parts to make structural funcionalizations to xenobiotics compounds. Microbial transformations are characterized by versatility, efficiency, regioselectivity, chemoselectivity and enantioselectivity of the enzymatic processes involved. In a single process one or more products can be obtained and they occur under mild conditions considered environmentally friendly and can be placed in the field of white biotechnology and green chemistry. The microorganisms are capable of transforming a wide variety of organic compounds, in especial phytopatogenic fungi are an interesting group because of the large number of genera and species that form and the variety of enzymatic processes that can be achieved by them. In this article, it is described the biotransformation of many sesquiterpenes by different fungal species applied towards the obtaining of derivatives. The transformation of these compounds can result in compounds with enhanced biological activities with potential applications in various industrial sectors such as the pharmaceutical, agricultural, food, etc.