show Abstracthide AbstractSap sucking insects cause severe damage to both plant of field as well as transgenic house in temperate and tropical regions. There are several reports where author have shown the changes at transcriptome level after infestation with these sap sucking insect in model plant, but high infestation time point and microarray based technology they used. Here we did a comparative transcriptome sequencing of Gossypium hirsutum L. (cotton) leaves to differentiate qualitatively and quantitatively response of cotton plant at transcriptomic level in aphid and whiteflies infestation at 2 hrs and 24 hrs with control.