Phylogenetic relationships of Paecilomyces sect. Isarioidea species were analysed using the β-tubulin gene and ITS rDNA. Maximum parsimony analyses showed that the section does not form a natural taxonomic group and is polyphyletic within the Hypocreales. However, a group was recognized, designated as the Isaria clade, to be monophyletic comprising of the following Paecilomyces species: P. amoeneroseus, P. cateniannulatus, P. cateniobliquus, P. cicadae, P. coleopterorus, P. farinosus, P. fumosoroseus, P. ghanensis, P. javanicus and P. tenuipes. Some of these species have teleomorphs in Cordyceps.