Abstract: RFLP, RAPD and AFLP analysis were performed between Nongken 58S and 1514, two varieties of rice, and their bulked extremes of F2. The rate of polymorphism and positive marker linked to target gene was compared. The results indicated that the rates of polymorphism and positive marker of RFLP, RAPD and AFLP are 19.93%, 5.23%；11.17%, 0.76% and 86.47%, 7.52%, respectively. The rate of polymorphism and positive marker of AFLP is highest in the three kinds of molecular marker systems. It was discussed that the advantages and disadvantages, and application of the three kinds of molecular marker systems in constructing a high resolution map of a specific chromosome region and selecting linkage markers to target gene.