Influencing factors which affected ISSR-PCR in apple were studied and primers selected in this study. The results showed that 25μl reaction volume including 0.8μmol/L primer and 20ng DNA was proper in ISSR-PCR of apple. The suitable annealing temperature could reduce non-specific amplification and improve polymorphism and differences in PCR product. Most of the annealing temperature was 2-4℃ lower than Tm. 17 primers were selected from 112 ISSR primers,and a total of 113 DNA bands were amplified,74 of which（65.5%） were polymorphic.