The wheat stripe (yellow) rust caused by Puccinia striiformis f.sp. tritici (Pst) of wheat is a major threat to wheat production worldwide. The breakdown in resistance of certain major genes and an emergence of aggressive races of Pst are causing serious concerns in main wheat growing areas of the world. Genetic resources are key to finding new sources of resistance and the associated QTLs for use in breeding high yielding and rust resistant germplasm. In this study, a panel comprising of 600 bread wheat landraces collected from Iran, Turkey, Syria, Iraq, Jordan, Greece, Spain, and Palestine preserved at ICARDA genebank were evaluated for seedling and adult plant resistance against PstS2 and “Warrior” races of Pst at Regional Cereal Rust Research Center, Izmir, Turkey. The panel was genotyped using DArTseq molecular technique. The genome wide association study (GWAS) was carried out using the Mixed Linear Model (MLM) as implemented in the genome association and prediction integrated tool (GAPIT). Genotypic data was filtered and a set of 25,169 DArTseq SNP’s were used in final analysis. A total of 50 markers were found to be associated with seedling stage resistance against the two races of which four were found to be highly significant (Bonferroni correction p < 0.001). Associated markers to seedling resistance were located on chromosomes 1B, 1D, 2A, 2B, 2D, 3A, 3B, 3D, 4A, 4B, 4D, 5B, 5D, 6A, 6B, 6D, 7A, 7B, 7D, and other unknown regions. Marker associated to adult plant resistance were found to be located on chromosomes 1A, 1B, 1D, 2A, 2D, 3B, 3D, 4B, 5A, 5B, 6A, 6B, 7A and unknown chromosome regions with highest number of markers located on chromosome 4B and 7A. The threshold of significance for all SNP-trait associations was determined by the false discovery rate (q) < 0.01. Some of the identified linked markers were located at same chromosome locations of previously reported Yr-genes. Associated markers with the resistance to these two races in new chromosome locations might indicate identification of new sources of resistance and hence potential new genes/QTL’s linked to stripe rust which can be used in enhancement of durable resistance to stripe rust.