Moisture deficit stress is a major environmental factor affecting crop productivity, including wheat, one of the world's most vital staple crops. Understanding the genetic basis of seed morphological traits under moisture deficit stress condition is essential for developing climate-resilient wheat cultivars. We used 193 wheat genotypic panel and 35,143 genetic markers to assess seven seed morphological traits, including area size, perimeter length, seed length, seed width, circularity of seed, length-to-width ratio and the distance between the intersection of length and width of seed and the centre of gravity. We also measured the thousand seed weight as a quality trait. Our findings revealed 37 associations between markers and these seed traits across 18 chromosomes. Remarkably 26 of these associations explained the 10% of the phenotypic variation in the traits under moisture stress conditions. These marker-trait associations reveal genes responsive to moisture deficit stress, offering promise for developing climate-resilient wheat varieties. The genomic regions linked to these traits could be utilized for marker-assisted selection, ultimately boosting wheat productivity in challenging climates.