The ITS II and the first part of the LSU rDNA were amplified from 26 isolates within the genus Entomophthora. The specificity of the primers allowed the use of both in vivo and in vitro material. Size polymorphism and long amplification of the ITS II regions, ranging from 1200 to 2000 bp, were observed. The PCR-products were cut with eight different restriction endonucleases and analysed by UPGMA, one analysis from each of the two regions. Conidial morphology was of predictive value for the overall taxonomy of the genus Entomophthora, as the genus clustered together in the analysis of the LSU rDNA. In both analyses the E. muscae complex clustered into three different clades, which support the validity of E. schizophorae and E. syrphi as separate species. Considerable variation was detected in the E. muscae clade, but it could not be grouped by host, geographic origin or conidial morphology, though the E. muscae s. str. isolates in both analyses grouped together. One isolate with E. muscae-like conidia found on Hymenoptera clustered out within the E. muscae clade, widening the host range for E. muscae significantly.