TheCordyceps militariscomplex, which is a special group in the genusCordyceps, is rich in species diversity and is widely distributed in nature. Throughout the investigations of arthropod-pathogenic fungi in the national reserves and in Vietnam parks, collections ofC. militarisattacking lepidopteran pupae or larvae were located in the soil and on the leaf litter. The phylogenetic analyses of the combined nrSSU, nrLSU,TEF,RPB1, andRPB2sequence data indicated that the fungal materials collected in Vietnam belonged toC. militarisand two hidden species in theC. militariscomplex. The phylogenetic analyses and morphological comparisons presented here strongly supported the descriptions ofC. polystromataandC. sapaensisas new taxa as well asC. militarisas a known species. The morphological characteristics of 11 species in theC. militariscomplex, which included two novel species and nine known taxa, were also compared.