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 200-fold more resistant to imidacloprid compared to a susceptible strain (S) as judged by LC50 values. The IR showed cross resistances to other neonicotinoid insecticides. IEF and 2DE analyses revealed that general esterase isozyme patterns in IR were almost identical to those of S. Nevertheless, a significantly overexpressed protein spot was detected in IR. To identify differentially expressed genes in IR, comparative transcriptome analyses based on GS-FLX were conducted using total RNAs extracted from both IR and S strains, which generated ca. 290 Mb reads for each strain. Generally, most nicotinic acetylcholine receptor subunit genes, such as alpha 2 and beta 1, were more transcribed in S than in IR. In contrast, only alpha 5 subunit gene was 1.8 fold more expressed in IR. Seven ATP-binding cassette (ABC) transporter genes were newly identified in A. gossypii, among which only ABCC9 gene was highly expressed in IR. Therefore, this ABCC subfamily, a member of the MRP subfamily which is involved in multi-drug resistance, could be one of the main factors associated with imidacloprid resistance in A. gossypii.