A forward cold induced subtracted cDNA library was constructed to identify the stress regulated genes in a high altitude cold desert-adapted species Cicer microphyllum, a wild relative of cultivated chickpea, distributed in western and trans-Himalayas. A total of 1,040 clones were obtained from the subtracted cDNA library. These clones were screened for presence of insert with colony PCR. A total of 523 clones were picked by colony PCR among which 300 clones were observed differentially expressed as per dot blot analysis. Differentially expressed clones were sequenced and assembled into clusters based on the presence of overlapping, identical, or similar sequences. A total of 283 ESTs were submitted in gene bank (accession numbers GO241043 to GO241326). BLAST analysis of these ESTs revealed its similarity for regulatory proteins like kinases, metallothionin, and enzymes/proteins with unknown functions. A cDNA encoding wound induced like protein, identified from this cold induced subtraction cDNA library, was full-length cloned using RACE and sequenced (accession number GQ914056). Southern blot of C. microphyllum indicated single copy of the gene in genome. Transcript expression profiling of this gene by quantitative real-time PCR and northern blot confirmed its up-regulation during low temperature stress. Further, in situ RNA hybridization also revealed cold (4°C) induced expression of the gene.