The cotton aphid, Aphis gossypii (Glover), is one of the most serious pest in seed potato and various vegetable cultivation. The imidacloprid-resistant strain (IR) was over 300-fold more resistant to imidacloprid compared to a susceptible strain (S) as judged by LC50 values. A highly imidacloprid-resistant local field population (L) was collected from cucumber at Gangwha island in 4th August 2011. Even though neonicotinoid insecticides especially imidacloprid were sprayed six times during June and July, aphid density was too high to be counted. To identify differentially expressed genes in IR or L, comparative transcriptome analyses based on GS-FLX were conducted using total RNAs extracted from IR, L and S strains. Futhermore, to search the resistance associated proteins in IR or L, comparative proteome analyses based on 2DE were conducted using total proteins extracted from IR, L and S strains. Few common candidate genes detected among IR and L such as ABC genes. Comparison of the nucleotide sequence of six nicotinic acetylcholine receptor (nAChR) subunit (alpha 1-5, beta 1) genes from IR, L and S strain revealed a point mutation in the loop D region of the nAChR beta 1 subunit of the IR, causing an arginine to threonine substitution (R81T). These mechanisms also reported in Myzus persicae and this amino acid change confers a vertebrate-like character to the insect nAChR and results in reduced sensitivity to neonicotinoids.