There is not enough information available on drought-modulated gene(s) in Gossypium arboreum, which can be a valuable gene pool for improving modern cotton cultivars. In the present work, differential display reverse transcriptase PCR (DDRT) was used to compare overall differences in gene expression between water-stressed and control plants. By screening 93 primer-pair combinations, the DDRT technique resulted in upregulation of 30 cDNA transcripts. Through reamplification and quality control assay, ten cDNA transcripts appeared false positive. The remaining 20-cDNA transcripts were extracted from the gel, reamplified, cloned and sequenced. Homology search revealed that six transcripts showed significant homology with known genes. Real-time RT-PCR showed that, among six transcripts, five showed significant overexpression in water-stressed leaves as compared to control. This is an important finding since there are only few reports of universal stress protein, and transposable elements are available in plants but none in cotton under drought condition.