Abstract: Different strains of H. marmoreus were genetically analyzed by use of Inter genicspacer 2 (IGS2) and the random amplified polymorphic DNA (RAPD) maker. Results showed that there was length heterogeneity on IGS2 of the 20 strains. The length range of IGS2 sequences was from 1150 to 1203bp. The similarity between sequences was about 95%. 11 out of 100 RAPD primers were selected according to the stability and difference of amplification bands. All the tested strains were amplified with the selected 11 primers and a total of 142bands were obtained, of which 134 bands showed polymorphism and the polymorphism rate was high. Results indicated that the RAPD bands varied from the strains and would become a molecular marker for strain identification or discrimination.