Five factors(Taq polymerase,Mg2+,dNTP,primer,DNA template) of Hordeum vulgare subsp.Vulgare(barley) ISSR amplification system were optimized using ISSR reaction system to analyze the evolutional relationship of barley.And then the optimum reaction system which contained 0.5 U Taq polymerase,1 μmol/L Mg2+,0.2 μmol/L dNTP,0.3 μmol/L primer,50 ng DNA template in a total volume of 25 μl amplification system was established.The optimum reaction system contributed greatly to use the ISSR-PCR technology to classify the quality of Hordeum vulgare subsp.Vulgare and mine the new genes.