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The Didymellaceae was established in 2009 to accommodate Ascochyta, Didymella and Phoma, as well as several related phoma-like genera. The family contains numerous plant pathogenic, saprobic and endophytic species associated with a wide range of hosts. Ascochyta and Phoma are morphologically difficult to distinguish, and species from both genera have in the past been linked to Didymella sexual morphs. The aim of the present study was to clarify the generic delimitation in Didymellaceae by combing multi-locus phylogenetic analyses based on ITS, LSU, rpb2 and tub2, and morphological observations. The resulting phylogenetic tree revealed 17 well-supported monophyletic clades in Didymellaceae, leading to the introduction of nine genera, three species, two nomina nova and 84 combinations. Furthermore, 11 epitypes and seven neotypes were designated to help stabilise the taxonomy and use of names. As a result of these data, Ascochyta, Didymella and Phoma were delineated as three distinct genera, and the generic circumscriptions of Ascochyta, Didymella, Epicoccum and Phoma emended. Furthermore, the genus Microsphaeropsis, which is morphologically distinct from the members of Didymellaceae, grouped basal to the Didymellaceae, for which a new family Microsphaeropsidaceae was introduced.