In this paper,the orthogonal design was used to optimize ISSR-PCR amplification system on pear in four levels of five factors(Taq DNA polymerase,Mg2+,DNA template,dNTP,and primer) respectively.The result of PCR was analyzed by software DPS,and the most suitable ISSR-PCR system for pear was established,it’s 20μL reaction system contained 1.0U Taq DNA polymerase,2.0 mmol.L-1 Mg2+,10~80ng DNA template,0.10 mmol.L-1 dNTPs,0.3 μmol.L-1 primer.The optimal annealing temperature for ISSR-PCR reaction was 55℃ propos...