Species of Melanospora are parasitic on or closely associated with other fungi. The morphological characters traditionally used to place Melanospora and the Ceratostomataceae in Sordariales do not agree with their placement in our phylogenetic study. The nuclear encoded small subunit ribosomal DNA (SSU nrDNA) grouped four species of Melanospora and several allied genera and species in Hypocreales, an order rich in mycoparasites. An analysis based on characters derived from deduced amino acids from the second largest subunit of the RNA polymerase II (RPB2) gene further supports the close relationship of Melanospora and Hypocreales. The nuclear encoded large subunit ribosomal DNA (LSU nrDNA) phylogeny inferred six groups for 40 species in Hypocreales and allied genera (Bionectria, Claviceps, Hypocrea, Nectria, and Niesslia). Four species of Melanospora, including the type, and two Sphaerodes species formed a basal clade. Scopinella was placed in a distinct clade. Two other allies of Melanospora, Syspastospora and Persiciospora, were closely related to or within the Hypocrea and Nectria groups, respectively. The study argues for the reclassification of taxa that previously were placed in the Sordariales.