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Soil salinity is a major environmental stress that adversely impacts the growth, development, productivity and quality of crop species, in particular, in arid and semi-arid regions. Identification of chromosomal regions associated with agronomic traits under salinity stress is crucial for improving salinity tolerance in wheat. GWAS and structure analyses were employed to evaluate 289 elite lines of the Wheat Association Mapping Initiative (WAMI) population under low (LS) and high (HS) salinity conditions using 15,737 SNP markers and seven agronomical traits. Evaluated genotypes responded differently to the different environments in all measured phenotypic traits, highlighting genetic diversity within the WAMI population in response to salt stress. Heritability degree ranged from moderate (37%) to high (88%). GWAS identified 118 and 120 significant associations between SNP markers and seven evaluated phenotypic traits under LS and HS conditions, respectively. Significant association of some markers with more than one phenotypic trait was observed, indicating possible pleiotropic or indirect effects. A high degree of significant linkage disequilibrium (> 52%) was observed among SNP markers on different chromosomes indicating epistatic interaction. The salt stress index (STI) exhibited a positive significant correlation to grain yield per plant (GYP) under both LS and HS conditions (R2 = 0.851–0.856). A linear regression between STI and GYP under HS conditions (GYPs) was identified, suggest that STI is the best tolerance index for predicting high yielding-genotypes. The results present the WAMI population as a valuable source for improving yield potential for salt tolerance in wheat. Furthermore, our findings emphasize that GWAS is a powerful tool in promoting wheat breeding through accurate identification of molecular markers significantly associated with agronomic traits, which is essential for marker-assisted breeding.