A diverse collection of wheat germplasm, consisting of 100 bread wheat lines with varying levels of salinity tolerance were evaluated based on incomplete block design (lattice) with two replications in field conditions. Plant material was screened for salinity tolerance under normal and saline field conditions. Subsequently in order to assess the haplotype diversity of QTLs attributed to salinity tolerance in wheat (Triticum aestivum), a collection of 30 extremes tolerant and sensitive genotypes among them were selected for genotyping on the basis of morphological, physiological and phenological traits. Genotyping was done using microsatellite markers which had been detected as the flanking regions of large effect QTLs attributed to salinity tolerance on chromosomes 2A, 4D and 3B. Combined analysis of saline and normal conditions revealed that genotypes showed highly significant responses. Association analysis of SSR markers with traits, showed markers Xcfa2121b, Xgwm10 and Xgwm296 on chromosome 2A and markers Xgwm194 and xgwm624 for chromosome 4D, had significant association with most of measured traits. Haplotype diversity analysis showed markers Xgwm10, Xgwm445, Xbarc353.2, Xgwm312, Xgwm515 and Xwmc296 on chromosome 2A as well as markers Xwmc326 and Xgwm345, Xbarc48.4 on chromosomes 3B and 4D were identified as the best markers attributed to salinity tolerance and they can be informative markers for improvement of salinity tolerance through marker-assisted selection programs.