Stem rust caused by Puccinia graminis f. sp. tritici Eriks. & Henn is the most destructive disease of durum and common wheat. The main focus of this study is to identify loci associated with stem rust resistance in durum wheat using association mapping and linkage mapping. A panel of 283 lines and 224 recombinant inbred lines (RILs) from a cross between ‘Reichenbachii’ and ‘DAKIYE’ developed by the durum wheat breeding program of the International Maize and Wheat Improvement Center (CIMMYT) were used for the study. The panel was evaluated against races TTKSK, TKTTF, JRCQC and TTRTF at the seedling stage and TKTTF and JRCQC in the field in Ethiopia from 2018 to 2019 for two seasons. The same panel was evaluated against bulk of multiple stem rust races prevalent in Ethiopia and Kenya from 2018 to 2019 in five environments. Genome-wide association study (GWAS) was conducted using 26,439 single nucleotide polymorphism (SNP) markers for seedling response (280 lines) and field response (283 lines) to stem rust. The RILs along with the two parents were evaluated for response to bulk of multiple stem rust races in Ethiopia and Kenya for two seasons from 2019 to 2020. Linkage analyses were conducted using 843 SNP markers for 175 lines. For GWAS of seedling response, a mixed linear model (MLM) identified 17 quantitative trait loci (QTL) of which eight were putatively novel while FarmCPU identified 20 QTL and 12 were likely novel. For field resistance to races TKTTF and JRCQC, MLM detected 19 QTL of which 12 were likely novel while FarmCPU detected 16 QTL and seven were putatively novel. For resistance to multiple Pgt races in East Africa, 160 significant marker-trait associations (MTAs) grouped into 42 QTL were identified using MLM and FarmCPU and 21 QTL were likely novel. From previously reported Sr genes, the regions of Sr7a, Sr8a, Sr8155B1, Sr11, Sr12, alleles of Sr13, Sr17, Sr22/Sr25, and Sr49 were identified. For the biparental population, composite interval mapping (CIM) identified three QTL on chromosomes 3B (QSr.cnl-3B), 4B (QSr.cnl-4B) and 7B (QSr.cnl-7B). These three QTL contributed by the resistant parent explained 4.7% to 15.3% of the phenotypic variation and all match previously reported loci. Lines with multiple-race stem rust resistance can be used as parents in durum wheat resistance breeding to stem rust and markers identified in the GWAS can be used in marker-assisted selection (MAS) once validated in a different population. Further study on the validation of allele specific markers and allelism tests in the Sr13 region of chromosome 6A is needed. Future evaluation of large numbers of durum wheat lines and searching for durable adult plant resistance gene is crucial in resistance breeding of durum wheat.