In order to reveal the differences between Cordyceps, Paecilomyces (= Isaria) and Nomuraea, we collected seven entomogenous fungi grown in natural field and analyzed the profiles of water-soluble constituents derived from some different sources of Cordyceps, Paecilomyces and Nomuraea by determination using capillary electrophoresis. C. sinensis and C. kyushuensis showed similar peak clusters of protein migrated at 5–7, 8–9, and 12–20 min. The peak clusters obtained from N. atypicola was similar to those of C. sinensis and C. kyushuensis. The water-soluble constituent clusters of C. militaris migrated at 5–9 and 10–15 min were partly different from those of other Cordyceps. It was also revealed that the P. tenuipes and P. cicadae showed lesser peak clusters rather than Cordyceps. These results indicated that the profiles of protein of these entomogenous fungi by capillary electrophoretic analysis could serve as fingerprints for classification and medicinal quality control of Cordyceps.