Cotton is an economically important crop that generates billions of dollars in annual revenue worldwide. Whitefly (Bemisia tabaci) and whitefly-transmitted cotton leaf curl disease (CLCuD) cause great damage to overall cotton production. Compared to widely cultivated cotton species Gossypium hirsutum, the diploid species G. arboreum is a natural source for resistance against CLCuD. However, the gene expression changes steered by whitefly and CLCuD infestation in G. arboreum and G. hirsutum and the interaction mechanisms of CLCuD to these cotton species remain to be elucidated. In the present study, RNA-Seq based transcriptomics have been subjected to elucidate the differential gene expression in G. arboreum and G. hirsutum under CLCuD infestation. G. arboreum plants were infested with CLCuD by graft and viruliferous whitefly-mediated inoculation. However, for G. hirsutum, CLCuD susceptible and resistant accession Mac7 were infested by whitefly-mediated CLCuD. RNA-Seq was done on plants from each experiment using Illumina HiSeq 2500 and data analysis identified differential gene expression in G. arboreum and G. hirsutum under CLCuD infestation. qRT-PCR, gene ontology enrichment, KEGG pathway analysis and homology searches were used for validation and functional annotation based characterization of identified genes in transcriptomic data in response to CLCuD. Several genes involved in disease resistance and pathogen defense were identified. Furthermore, coexpression network analysis on the RNA-Seq datasets, indicated the hub genes, showing their crucial role in defense or susceptibility of cotton in response to CLCuD. The important gene families identified in cotton under CLCuD stress include phytohormones, transcription factors, kinases, oxidative stress, membrane channel proteins, protein modifications, methylation and metabolism-related genes. Overall, it is concluded that the resulting datasets give inclusive insights into the cotton defense or susceptibility mechanisms under whiteflies and CLCuD infestation. This study reveals several candidate genes involved in a virus-host interaction that might be used for the control of whitefly, other sap-sucking insects and CLCuD in cotton