Traditionally, fungal taxonomy was based on observable phenotypic characters. Recent advances have driven taxonomic conclusions towards DNA-based approaches and these techniques have corresponding pros and cons. Species concepts must therefore rely on incorporated approaches of genotypic, phenotypic and physiological characters and chemotaxonomy. Examination and interpretation of morphological characters however vary from person to person. Standardized procedures are used in the taxonomic study of fungi and general practices of phenotypic approaches are herein outlined. It is not possible to detail all techniques for all fungi and thus, this paper emphasizes on microfungi. Specimen collection is the initial step in any taxonomic study and all taxonomic information are gathered from the specimens. Therefore, guidelines are provided for the collection, data recording and storage of specimens. Morphological examination, microscopy, photography and descriptions of specimens are important for fungal identification. Hence, techniques for staining, mounting and slide preparation are explained. In addition, obtaining pure cultures from specimens and maintaining those isolates for future studies are challenging. Isolation techniques are numerous and often complicated. Good techniques need to isolate a maximum number of strains from a specimen and obtain the desired taxon, while excluding all others. Methods to isolate microfungi including basal fungi, hyphomycetes, coelomycetes, ascomycetes, plant pathogens, soil fungi, air-borne fungi, epiphytes and endophytes are detailed herein. Sporulating cultures are useful to describe the morphological characters of relevant fungi, but sometimes these characters are absent or difficult to find on natural substrates and it is also difficult to link same fungal organisms based on sexual and asexual morphs. The techniques that induce sporulation of different fungal groups are explained and discussed. Specimens, protologues or descriptions, diagrams, illustrations, cultures and DNA sequences need to be deposited at accessible repositories and guidelines are provided for such deposition. The available data are used in future studies. Furthermore, preservation of cultures and specimens is essential. Cultures are used in DNA extraction, mating or cultivation studies, sporulation and metabolites extraction. Colony characters are often significant from each other and sporulated, dry cultures and specimens represent the type status of the desired fungus. Therefore, culture and specimen preservation techniques of different fungal groups are discussed.
