Fungal diseases, such as stripe rust, are major bottlenecks in Ethiopian wheat production. They can significantly reduce yields and impact regional food security. To enhance Ethiopian wheat production, incorporating genetically resistant cultivars into breeding programs is essential. Accordingly, this study aimed at exploring the genome-wide association of seedling resistance in 178 wheat genotypes to identify genetic markers linked to yellow rust resistance. The panel was phenotyped for yellow rust seedling resistance at Kulumsa Agricultural Research Centre Pathology Laboratory. Additionally, the association panel was genotyped using the genotyping-by-sequencing (GBS) platform and a total of 6,788 polymorphic SNPs were used in genome-wide association analysis to identify effective yellow rust resistance genes. The Genome Association and Prediction Integrated Tool (GAPIT) was used to analyze marker-trait associations. The overall linkage disequilibrium (LD) decreased within an average physical distance of 31.44 Mbp at r