Leaf and stripe rusts are severe foliar diseases of wheat worldwide. Leaf and stripe rust resistant introgression lines were developed through induced homoeologous chromosome pairing between 5D of wheat and 5M^g of Aegilops geniculata. Genomic in situ hybridization with Aegilops comosa DNA as probe showed three different types of introgressions. All three types of introgression lines showed similar and complete resistance to the most virulent and prevalent races of leaf rust and stripe rust in Kansas. One resistant line with a cytologically undetectable introgressed segment was used for molecular characterization of leaf and stripe rust resistance. Diagnostic polymorphisms between the alien segment and recipient parent were identified using physically mapped RFLP and EST probes. Mapping revealed that the alien introgression conferring resistance to leaf and stripe rusts is less than 5% of the chromosome arm 5DS. Genetic mapping in an F₂ population of T5DL.5DS-5M^gS(0.95) showed that rust resistance is monogenically inherited. Molecular mapping in the above F₂ mapping population indicated that the translocated segment of Ae. geniculata did not recombine with wheat chromosome arm 5DS. Two diagnostic RFLP markers that co-segregated with the rust resistant introgression were identified. The unique and new map location of the resistant introgression on chromosome arm 5DS suggests that in the introgression line T5DL.5DS-5M^gS(0.95) the leaf rust and stripe rust resistance genes are novel and are designated as Lr57 and Yr40, respectively. The rust resistant introgression line T5DL.5DS-5M^gS(0.95) which has no obvious effects on plant growth and development, was used to transfer the novel leaf rust and stripe rust resistance genes into elite winter and spring wheat cultivars.