Eleven isolates within four species of the entomogenous fungus Aschersonia from China, the USA, Japan, the Philippines, Malaysia and Columbia were characterized using 17 RAPD primers. Genetic diversity among these strains of Aschersonia was found. The clustering results showed that the genetic variability among interspecies was more than that among intraspecies of Aschersonia. In the constructed phylogenetic tree, these isolates were not clustered according to their geographic origins or hosts. Furthermore, sequences of the divergent domain at the 5′-end of the large subunit (LSU) in nuclear rRNA from the mitosporic entomogenous fungi were employed to analyse the phylogenetic relationships of 11 Aschersonia isolates. The relationships of interspecies or intraspecies shown in the phylogenetic tree were almost consistent with the results of the morphological study. Different species isolated from different geographic origins could be clearly distinguished in the tree. But there were no close relationships among species isolated from the same family or order of insect hosts. The tree indicated that isolate Aa, belonging to A. aleyrodis, was the same as Aa992 and Aa3.4485. Moreover, results of RAPD analyses were consistent with those of LSU nuclear rDNA analysis for the same isolates tested, which consequently indicates that both methods can be independently applied for classification and identification of Aschersonia.