Incident of homoeologous chromosome pairing and exchange could occurred in hexaploid wheat under ph1b genetic background and producing compensable and genetic stable recombinants. So transfering the alien chromosome into a ph1b background is the basis of generating the recombinants on the target chromosomes. However, it is difficult to identify a ph1b genotype rely on its phenotype. In present study, the target plants with ph1b containing the alien chromosome 2Ai-2 were selected effectively by using molecular markers Mads (on the deletion region of ph1b), P4 and P68 (on the alien chromosome) when screening the F2 population of CSph1b crossing with N420，a wheat-Thinopyrum intermedium 2B（2Ai-2）substitution line, and their derive F5 lines.