The partial rust resistance genes and have been used extensively in wheat ( L.) improvement, as they confer exceptional durability. Interestingly, the resistance of is associated with the expression of leaf tip necrosis (LTN) and with pseudo-black chaff (PBC). Genome-wide association mapping using CIMMYT’s stem rust resistance screening nursery (SRRSN) wheat lines was done to identify genotyping-by-sequencing (GBS) markers linked to LTN and PBC. Phenotyping for these traits was done in Ithaca, New York (fall 2011); Njoro, Kenya (main and off-seasons, 2012), and Wellington, India (winter, 2013). Using the mixed linear model (MLM), 18 GBS markers were significantly associated with LTN. While some markers were linked to loci where the durable leaf rust resistance genes (7DS), (1BL), and (7BL) were mapped, significant associations were also detected with other loci on 2BL, 5B, 3BS, 4BS, and 7BS. Twelve GBS markers linked to the locus (3BS) and loci on 2DS, 4AL, and 7DS were significantly associated with PBC. This study provides insight into the complex genetic control of LTN and PBC. Further efforts to validate and study these loci might aid in determining the nature of their association with durable resistance.