Kenaf male sterility breeding gave a new method for the use of kenaf heterosis. The maker of genic-male sterility genes in kenaf is used in the chosen of good sterile line or maintainer line. Using per-plant back crossing to choose sterile line and using BSA to screen ISSR primer. Using plant AT-1found by kenaf breeding research group of institute of bast fiber crops Chinese academy of agricultural sciences in Sanya of Hainan province were used as female parent in crossing with 15-4, 04K1 and then backcrossed four times with male parent in order to select two high sterile male sterility. The DNA of every plant was extracted by CTAB to constitute the gene pool by BSA. Applying the ISSR technique we analysised the two gene pool. Finally we found a primer which can show the difference between the sterile gene pool and fertile gene pool. The ISSR primer is U859. The result showed the male sterility is cytoplasmic nuclear interaction male sterile, male sterility steady, and the ISSR primer U859 is linked with genic-male sterility.