Leaf rust and stripe rust are among the most damaging diseases of wheat worldwide. Wheat cultivation based on a limited number of rust resistance genes deployed over vast areas facilitates the emergence of new pathotypes warranting a continuous deployment of new resistance genes. Wild relatives, landraces and early domesticates harbour rich genetic diversity. However, their use is limited due to difficulties encountered in introgression breeding, suppressed recombination and linkage drag. In this paper, we develop alien introgression specific SNP markers from flow-sorted chromosome sequence and successfully identified candidate genes of Aegilops umbellulata derived leaf rust and stripe rust resistance genes Lr76 and Yr70. Short arm of Ae.umbellulata chromosome 5U (5US) from its ditelosomic addition line, recombinant chromosome 5D (5Drec) from wheat-Ae. umbellulata introgression line pau16057 along with 5DRPof the recurrent parent WL711 were flow-sorted and paired-end sequenced. Chromosome 5US reads were mapped against the reference Chinese Spring chromosome 5D sequence and alien specific SNPs were identified. Chromosome 5Drecand 5DRP sequences were de novo assembled and alien introgression specific markers were designed bys electing the SNPs, both between 5U and 5D and between 5U/5D and 5A/5B, to create genome-specific KASP markers. Overall, 27 KASP markers were mapped in a high resolution mapping population consisting of 1,404 F5 RILs. The mapping population was phenotyped for leaf rust and stripe rust resistance confirming the single gene segregation each for Lr76 and Yr70. The physical order of the SNPs on pau16057 was defined by projecting the 27 SNPs against the IWGSC RefSeq v1.0 sequence. Based on this physical map, we determined the size of the Ae. Umbellulata introgression to be 9.47 Mb on distal most end of short arm of 5D. This non-recombining 9.47 Mb alien segment carries six NB-LRR encoding genes based on IWGSC RefSeq v1.1 gene models. Presence of SNPs and other sequence variations in these six NB-LRR genes between pau16057 and WL711 suggests that they are likely candidates for Lr76and Yr70.