Powdery mildew-resistant wheat lines, Tra.R9002 with rye chromatin and Tra.V149 with Haynaldia villosa chromatin, were crossed to combine their different powdery mildew-resistant genes in the wheat genetic background. In the F 5 generation of Tra.R9002 × Tra.V149, a highly powdery mildew-resistant line W159 was selected according to its chromosome number 2n = 41 ~ 42. In the F 6 line W159-9 which was immune to powdery mildew, one pair of rye chromosomes and one pair of wheat-H. villosa translocated chromosomes were identified simultaneously by multicolor fluorescence genomic in situ hybridization in the wheat genetic background (chromosome number 2n = 42). Through C-banding and a sequential C-banding analysis after genomic in situ hybridization, the rye chromosomes were identified as 5R and the wheat-H. villosa translocated chromosomes were identified as 6VS-6AL. This indicates that W159-9 carries two powdery mildew-resistant genes of Pm4 on 5R and Pm21 on 6VS. The wheat chromosomes absent in W159-9 were identified as the 6AS and 5D. On the other hand, seven out of 17 progenies of another F 6 line W159-3 possessed 5R and 6VS-6AL chromosomes. These materials could be used for acquiring stable multiple powdery mildew-resistance in wheat breeding programs.