Cotton Leaf Curl Virus (CLCuV) is mainly one of the ruthless cause of cotton damage in Pakistan for which, until now, no passable therapy is available. In my present work, the local tolerant cultivar of Gossypium hirsutum (CIM-482) was initially tested via cotton leaf curl virus disease (CLCuD) epidemiological studies using reported disease rating scale and molecular diagnostic PCR technique. A susceptible cotton cultivar (S-12) was also used as inoculum source during disease optimization and as positive control for CLCuV infection in molecular detection of CLCuV from experimental plants. Disease epidemiological studies and molecular diagnostics confirmed CIM-482 as highly tolerant and S-12 as highly susceptible cotton variety. For the identification of CLCuV inducible genes, comparison of gene expression between control and tolerant plants was carried out using Differential Display Reverse Transcriptase PCR (DDRT) approach. Screening through 99 primer-pair combinations of 15 arbitrary and 12 anchored primers resulted in up-regulation of 42 cDNA transcripts from the tolerant samples which consistently displayed high differential intensity in comparison to control under disease stress. Only 18 differentially expressed transcripts (DETs) ranging in size from 103-1145bp were screened out as induced gene fragments; the other 24 were abandoned since false positives through reamplification, cloning & sequencing. The identified transcripts are reported first time against CLCuV infectivity and submitted as novel ESTs to GenBank database with accession numbers JZ495600- JZ495613. Homology search revealed that out of 18 transcripts, 14 showed very significant homologies with reported gene/ protein sequences while the rest of 4 transcripts remained uncharacterized due to non-significant homology with any of the known genes/proteins. The mRNA expression profiling via real time PCR of DETs also revealed that most of the transcripts showed up-regulated expression in tolerant samples as compared to controls except that of DET3 (P2T6a) and DET10 (P5T4b) which showed non-significant expression in disease tolerance. On the basis of highly up-regulated expression profile of DET17, transposon filtration and significant homology of transcript DET17 (P9T6a) with Gossypium arboreum protein, supposedly involved against CLCuV disease, it was selected and full length gene, G. hirsutum DNA-binding disease resistance RPS2-like gene (GhRPS2), with accession number KR809372, amplification was carried out through RACE (Rapid Amplification of cDNA Ends). A nucleotide sequence of 2677bp generated of 767 amino acids long open reading frame, which has 87.19kDa protein. It also has an upstream 5‟-UTR of 204bp and a downstream 3‟-UTR sequence of 169bp. The gene expression level was also confirmed and evaluated by real-time PCR which revealed high expression as compared to CLCuV diseased leaves. The genomic DNA PCR of full-length gene revealed that no introns were detected in the protein encoding sequence of GhRPS2 gene. Gene homology studies using bioinformatics tools depicted that GhRPS2 protein possessed high percentage similarity within the same taxon ranging from 98% to 92% with predicted disease resistance proteins of Gossypium spp. (G. hirsutum, G. arboreum and G. raimondii). It also exhibited 85% similarity with predicted bHLH transcription factors of above mentioned Gossypium spp. These percentage similarities are elevated enough for consideration of GhRPS2 protein to be DNA-binding protein family member, conferring disease resistance. The consensus sequences of two functional protein domains were found in the GhRPS2 protein .i.e., Leucine rich-repeat (LRR) domain and basic-helix loop helix (bHLH) DNA-binding protein domain. InterProScan results revealed the predicted GhRPS2 protein to be a member of transcription factor-related protein family. The diverse online sub cellular localization servers depicted that GhRPS2 protein might be localized in nucleus and cell membrane. The functional annotation of GhRPS2 sequence via Blast2Go analysis revealed its significant homology with disease resistance RPS-2 like protein of Gossypium arboreum (KHG12782). G. arboreum was also found to be the top hit species with highest similarity index. Functional annotation of full-length gene (GhRPS2) at molecular level depicted that it is involved mainly in binding activity with protein and nucleic acids, having dimerization capability for proteins and transcriptional regulation while binding with DNA. The signaling pathway map of GhRPS2 gene, identified using KEGG pathway database clearly indicated a signaling map related to plant-pathogen interactions. The likely function of GhRPS2 gene from this pathway map was revealed to be in the effector-triggered immunity. RPS2 gene (KEGG id: K13459) in combination with other defense related genes ultimately led to hypersensitive response (HR) which itself is a defense mechanism against pathogenic infections in plants. The tissue-specific expression profiling of GhRPS2 gene via real-time PCR from leaf, root & stem tissues which clearly displayed high expression of GhRPS2 in leaf tissue in comparison to stem and roots.