The genus Thelonectria and related species with Cylindrocarpon-like anamorphs are a group of perithecial ascomycetes in the family Nectriaceae that occur as saprobes and in few cases as pathogens of hardwood trees, shrubs or other plant substrates. Despite of being a key component of forest ecosystems around the world, species relationships and distribution are largely unknown. The objectives of this study were to: 1) infer species level phylogenetic relationships of the genus Thelonectria and related species with Cylindrocarpon-like anamorphs with uncertain classification, testing monophyly of each one of the groups studied; 2) delimit taxa, establishing taxon circumscriptions and providing brief descriptions; 3) resolve nomenclatural issues by identifying redundantly used names and synonyms; 4) provide identification tools, specifically, diagnostic keys and molecular data that can be used further as molecular barcodes; 4) provide distribution data and to take the first steps into the identification of speciation patterns observed in these fungi. To achieve these goals, herbarium materials, as well as freshly collected material obtained from the field or from fungal repositories were compared using phylogenetic analyses of multiple loci, morphology and geographic distribution. This research resulted in the narrower circumscription of the genus Thelonectria, not to contain one of the most common species in the group, T. jungneri. According to the results of the phylogenetic analyses it was found T. jungneri is a segregating clade that needs to be recognized as a different genus. For the genus Thelonectria, a total of 31 new species were described, and three new genera, closely related to Thelonectria were created to accommodate the diversity of other species with Cylindrocarpon-like anamorphs: Cinnamonectria gen nov. with C. cinnamomea as type taxon, Macronectria gen. nov. with M. jungneri as type taxon, and Tumenectria gen. nov. with T. laetidisca as type taxon. Species in this group of fungi present extensive morphological conservationism, representing a challenge for species identification without the use of molecular techniques, however offering a great opportunity to explore mechanisms of speciation and evolutionary diversification.