Fungi are eukaryotic organisms known to inhabit almost all ecological niches of the Earth and have the ability to utilise various solid substrates as a consequence of diversity of their biological and biochemical evolution. Some of the solid substrates utilised by fungi are dead and decaying material, including herbivore dung (saprophytic and coprophilous fungi), live plants (endophytic, parasitic, and mycorrhizal fungi), lichens (lichenicolous and endolichenic fungi), and insects (entomopathogenic fungi).

A characteristic feature of many of these fungi, especially those that exhibit filamentous growth and have a relatively complex morphology, is their ability to produce secondary metabolites. Soilborne, parasitic, and saprophytic fungal sources are relatively well investigated with regard to their secondary metabolites, and currently there is intense interest in secondary metabolites of symbiotic fungi that live in association with land plants, insects, lichens, and marine organisms. In contrast to primary metabolites such as proteins, DNA, RNA, polysaccharides, and so on, which occur universally, secondary metabolites are small-molecule organic compounds found restricted to a particular species, genus, or family. Thus, the presence or absence of certain secondary metabolites has been used successfully in the classification (chemotaxonomy) of large ascomycete genera (including Alternaria, Aspergillus, Fusarium, Hypoxylon, Penicillium, Stachybotrys, and Xylaria) and in a few genera of basidiomycetes.

Many secondary metabolites are not involved directly in the normal growth, development, or reproduction of the fungus in which they occur, but they may play an important role in ecological interactions with other organisms. For this reason, many fungal secondary metabolites exhibit useful biological activities and are of interest to the pharmaceutical, food, and agrochemical industries. Production of secondary metabolites often occurs after fungal growth has ceased as a result of nutrient limitations but with an excess carbon source available, making it possible to manipulate their formation. It is intriguing that some endophytic fungi are capable of producing secondary metabolites previously known from plants. Noteworthy examples include production of two clinically important anticancer drugs, paclitaxel (Taxol^®) and camptothecin, by Taxomyces andreanae and Nothapodytes foetida, respectively, and a synthetic precursor of an anticancer drug, podophyllotoxin, by Phialocephala fortinii.