Abstract: Abstract:. The main factors affecting IRAP-PCR amplification were optimized in order to develop inter-retrotransposon amplified polymorphism marker and to establish stable IRAP reaction system in Lentinula edodes. The optimal IRAP-PCR system was as follows, within 20μl reaction system, there were 30ng template DNA, 0.3μmol/L primer, 0.3mmol/L dNTPs, 2.0mmol/L Mg2+ and 0.75U Taq DNA polymerase. The optimal annealing temperature was determined as 56.1℃ by gradient PCR. Based on the optimal IRAP-PCR system, primer combination LTR1L and MarY1L was used to amplify genomic DNA of 18 strains. Results indicated that the optimal IRAP-PCR system is reliable.