This study utilized combined linkage analysis and association mapping in wheat to identify genomic regions associated with both yield and drought tolerance. Evaluating 304 accessions under well-watered and rain-fed water stress conditions, the research pinpointed 11 co-localized genomic regions related to yield traits and drought response values. Notably, a region on chromosome 2D associated with thousand kernel weight (TKW) was identified, with a key candidate gene, TraesCS2D02G142500. The study highlights molecular targets, such as a rare haplotype (Hap-2), offering insights for breeding high-yield, drought-tolerant wheat varieties.