Entomopathogenic fungi used in the present study were Metarhizium anisopliae, Beauveria bassiana and Paecilomyces fumosoroseus. The first fungus was isolated from the Rhynhophorus ferruginens in Ismailiya governorate, the second from the white fly in the Sharkia and the third from Aphis gossypii in Al-Fayoom governorate. Beauveria colonies are usually slow growing, downy, at first white but later often becoming yellow. The spores as balls represent dense clusters of large numbers of conidiogenous cells and conidia. Paecilomyces colonies are usually slow growing, at first white but later often becoming rosy-tan to smoky-pink (or Grey) in mass. Ovoid to elongate. Metarhizium colonies are usually strong growing, olivaceous green with yellowish color in reverse. yellowished green in mass. RAPD amplified DNA products using 5 primers differentiated 3 isolates of entomopathogenic fungi belonging to different genera collected from different locations and host insects. Total of 91 amplified fragments generated 81 polymorphic bands can be used as RAPD markers. There are 81 specific markers out of 137 total amplified fragments. RAPD markers were found to be useful as isolate specific marker. The results showed the specific markers for the 3 entomopathogenic fungi isolates resulting from RAPD-PCR analysis. B. bassiana isolate exhibit 18 positive amplified fragments and 9 negative, while P. fumosoroseus isolate generated 22 positive amplified fragments as a highest number of specific positive markers and 12 negative amplified fragments. As well M. anisopliae isolate showed 15 positive amplified fragments and 8 negative. The proteins of three entomopathogenic isolates were extracted from their mycelium and fractionated by SDS-PAGE. The proteins of B. bassiana, P. fumosoroseus and M. anisopliae were separated into 11, 4 and 5 bands respectively.