The partial rust resistance genes Lr34 and Sr2 have been used extensively in wheat improvement as they confer exceptional durability. Interestingly, the resistance of Lr34 is associated with the expression of leaf tip necrosis (Ltn) and Sr2 with pseudo black chaff (Pbc). Though previous studies have detected several QTL's linked to these traits, their genetic basis is still intriguing. Hence, association mapping was employed in this study for CIMMYT's Stem Rust Resistance Screening Nursery wheat lines to identify Genotyping by Sequencing (GBS) markers linked to Ltn and Pbc. Phenotyping for these traits was done in Ithaca, U.S.A. (Fall 2011); Njoro, Njoro (Summer and Fall 2012) and Wellington, India (Fall and Winter 2012).Using the Q + K matrix, 21 GBS markers were identified to be significantly associated with Ltn. While some of them were linked to loci where the durable leaf rust resistance genes Lr34 (7DS), Lr46 (1BL), Lr67 (4DL), Lr68 (7BL) were mapped, significant associations were also detected with loci previously known to interact with Lr34 (2BL and 5B) and few other loci (3BS, 3D, 5A and 7BS). On the other hand, 15 GBS markers were significantly a ssociated with Pbc. Besides the Sr2 locus (3BS) which was highly consistent, a locus previously identified to be linked to stem rust resistance (2BL) and other loci (2DS, 4A, 6AS and 7DS) were identified. Thus, this study provides a better insight into the genetic control of Ltn and Pbc. Further efforts to fine map and characterize these loci might aid in determining the underlying mechanism of their association with durable resistance.