Coelomycetes is a general term for asexual fungi which includes many important pathogens and species also used in biocontrol, biotechnology and bioremediation. Traditional classification of coelomycetes was based on morphology and was thus subjective, often resulting in artificial generic and species boundaries. Molecular based classification is now available to determine the phylogeny of species and genera. This has revolutionized our understanding of relationships between species and linked genera with their teleomorphs and placed them in a higher taxonomic framework. However, despite such advances approximately only 256 (26%) of the 992 coelomycetous genera are linked to their sexual stage, 105 (11%) are linked to a family or order, while for 631 genera (63%) no linkage is available. In this paper we detail how the taxonomy of coelomycetes has developed, examine some important phytopathogenic genera, and explore their applications.