Background <p>Soil acidity associated with aluminium toxicity is a major abiotic factors limiting durum wheat production in the highland areas of Ethiopia. Selection and use of Al tolerant genotypes is a sustainable strategy for boosting durum wheat production on acidic soils.</p> Methods <p>This study aimed to identify aluminum-tolerant durum wheat genotypes and associated genomic regions by evaluating 300 genotypes under both Al-stressed and non-stressed hydroponic conditions. Genome-wide association was estimated using 10,000 SNP markers for almunium stress indices and traits both in stress and non-stress conditions.</p> Results <p>The analysis of variance revealed highly significant differences among the genotypes for all studied traits. Alumimuim stress indices were estimated using nine methods in root and shoot tratis. Among eight stress indices, correlation analysis identified mean productivity, geometric mean productivity and aluminum adoption indices as effective measure for selecting aluminum tolerance genotypes. Genotypes grouped in to three major cluster based on their mean productivity, geometric mean productivity, aluminum adoption indices and traits in both almunium stress and non-stress conditions. Cluster one (20 genotypes) identified as aluminum tolerance group. Cluster two contain 30 moderatly tolerant genotypes and cluster three comprised 250 susceptible genotypes. Based on the functional annotations, 40 candidate genes associated with Al tolerance were identified using 10 QTNs detected by more than two model.</p> Conclusions <p>The functional characterization of these identified genes offers essential insights into the underlying genetic mechanisms that govern the response of durum wheat genotypes to aluminum stress. This knowledge offers a significant opportunity for the development of improved, aluminum-tolerant durum wheat varieties through further genetic research.</p>