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The present study evaluated three wheat genotypes (SD-28, SD-32 and Chirya-1) were evaluated for physiological attributes like Relative Water Content, Proline Content, Membrane Stability Index and Chlorophyll Content where Opata was used as a control check under three different levels of drought stress (100% FC, 80% FC and 60% FC). Results revealed that chlorophyll content was significantly affected under stressed conditions in all the studied genotypes and genotypes. Molecular diagnosis of the selected wheat genotypes and genotypes was carried out with RT-PCR using expression profile of 06 genes (TaLhca1, TaLhca2, TaLhca3, TaLhcb1, TaLhcb4 and TaLhcb6) that encodes for LHCI and LHCII proteins. RT–PCR indicated variable expression of the selected genes in response to different level of drought stress. The results obtained clearly showed the relation between genotypes and severity of drought stress condition. Among the studied genotypes Chirya-1 and SD-28 performed well with higher level of gene expression under drought stress condition; and may be considered drought tolerant genotypes with potential to enrich the genetic background of locally adapted wheat lines against drought stress.