A molecular phylogenetic study of selected species of three sub-genera of the genus Cordyceps was undertaken, along with representatives of the genera Akanthomyces, Aschersonia, Gibellula, Hymenostilbe, Hypocrella, Nomuraea, and Torrubiella, to examine their inter-relationship. Phylogenetic analyses of the data indicated that the Clavicipitaceae form a monophyletic group within the Hypocreales, while the monophyly of Cordyceps was not supported. Four clades were identified: Cor. militaris/Cor. pseudamilitaris; Cor. irangiensis/Cor. sphecocephala; Cor. intermedia/Cor. capitata; and Cor. cylindrica/Nom. atypicola. The sub-genus Neacordyceps was shown to be monophyletic while the sub-genera Eucordyceps and Ophiocordyceps do not form monophyletic groups. The genus Hypocrella appeared monophyletic, and radiated after the formation of the genera Cordyceps, and Torrubiella. Akanthomyces arachnophilus and Gi. pulchra, anamorphs of Torrubiella species, formed a distinct clade that was separate from one formed by the scale insect pathogens, To. luteorastrata and Paecilomyces cinnamomeus, suggesting that this genus may be polyphyletic.