Based on morphology and DNA sequence data the taxonomic relationships of Microdochium, Monographella and Idriella were reassessed. Microdochium is morphologically and phylogenetically circumscribed, and the sexual genus Monographella treated as synonym on the basis that Microdochium has more species, is more commonly encountered, and more frequently used in literature. An epitype is designated for Microdochium phragmites, and several well-known species are redefined based on their morphology and DNA sequence data (LSU, ITS, BTUB and RPB2). Furthermore, the revision of Microdochium led to six new combinations (M. albescens, M. consociatum, M. fusariisporum, M. maydis, M. opuntiae and M. stevensonii) and six new species (M. citrinidiscum, M. colombiense, M. fisheri, M. neoqueenslandicum, M. seminicola and M. trichocladiopsis) being proposed. Microdochium s.str. belongs to a monophyletic clade, together with Idriella lunata and Selenodriella, representing a new family, Microdochiaceae, in Xylariales. Other species previously accommodated in Microdochium belong to different orders in the Ascomycota. Microdochium gracile belongs to Sordariomycetes (incertae sedis) and Paramicrodochium is proposed to accommodate this species. Microdochium tripsaci belongs to Ephelis in Clavicipitaceae, while M. fusarioides belongs to a new genus, Microdochiella in Orbiliales. Idriella s.str. is a monotypic genus phylogenetically closely related to Microdochium. Idriella s.l. separates into different genera in Xylariales (incertae sedis) including Castanediella, Selenodriella, Idriellopsis, Neoidriella and Paraidriella, the last three proposed here as new genera.