Doubled haploid populations of CD87/Katepwa, Cranbrook/Halberd, and Sunco/Tasman were assessed for seedling response to stem rust and stripe rust. The CD87/Katepwa population was also screened as adult plants in the field against stripe rust. The respective parents differed in presence or absence of various stem rust and stripe rust resistance genes. At least 4 resistance loci controlled adult plant resistance to stripe rust in the CD87/Katepwa population, and based on quantitative trait loci mapping results, two of these were contributed by CD87. Pedigree information indicated that these regions correspond to durable adult plant stripe rust resistance genes Yr18 and Yr29. Yr29 was mapped to the distal region of chromosome 1BL. The third gene, contributed by Katepwa, YrKat, was located in chromosome arm 2DS. Sr30 mapped distal to markers abg3 and P36/M61-170 in chromosome arm 5DL. Genes Yr7 and Pbc (completely linked with durable stem rust resistance gene Sr2) showed close associations with markers in chromosome arms 2BL and 3BS, respectively. A distally located genomic region in chromosome 6AS also affected the expression of Pbc. The temperature-sensitive stripe rust resistance gene, YrCK, carried by Sunco showed monogenic inheritance and was located in chromosome arm 2DS. Several markers showed complete association with Triticum timopheevi derived stem rust resistance gene Sr36. Microsatellite markers stm773 and gwm271A were validated on a set of wheat genotypes and were found to be diagnostic for the detection of Sr36. TheSr36-linked Xstm773 allele showed better amplification than the Sr36-linked Xgwm271A allele. These markers could be used for marker assisted identification of Sr36 in breeding populations.