The C. militaris belongs to entomopathogenic fungi, which have their specific sequences in internal transcribed spacer regions (ITS1 and ITS2) depending on species. In this study, to identify the phylogenetic relationship of the strain hybrided by mating of C. militaris, we compared DNA sequences of ITS regions and 5.8S ribosomal DNA (rDNA) repeat unit of hybrid strain and its parental strains. The result revealed that hybrid strains are C. militaris species. In addition, cordycepins produced by hybrid strains and other strains of C. militaris were analyzed by HPLC with 20 mM KH₂PO₄ of mobile phase and C-18 columns. The result indicated that the strain hybrided by mating produce higher concentration of phytochemical cordycepin than other C. militaris strains.