This study was carried out to identify the phylogenetic relationship and to know the distribution of the entomopathogenic fungi by comparing the DNA sequences of internal transcribed spacer regions (ITS1 and ITS2) and 5.8S ribosomal DNA (rDNA) repeat unit. The entomopathogenic fungi had their specific sequences in ITS1 and 2 regions depending on species. The comparison of the ITS sequences of standard strains indicated that the sequences ITS1 were more variable than those of ITS2. It seems that Paecilomyces tenuipes, Isaria japonicus and P. japonicus are the same species but called as different names because of very similar sequences, and unidentified Paecilomyces sp. KACC 40220 and KACC 40656 showed identical sequences to P. tenuipes. Thirty six strains of the commercial products of entomopathogenic fungi used in this study were divided into four groups by the phylogenetic analysis based on 5.85 rDNA and ITS regions. We found twenty-three strains were P. tenuipes / japonica, eleven strains were C. militaris, and other two strains were Beauveria bassiana and C. multiaxialis, respectively.