The cotton aphid, Aphis gossypii (Glover), is one of the most serious pest in the cultivation of various vegetables. A highly imidacloprid-resistant field population (CA-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. IEF and 2DE analyses revealed that general esterase isozyme (pI. 5) in CA-L were dramatically overexpressed and more isozyme spots identified in CA-L compared to susceptible (CA-S) strain. To identify differentially expressed genes in CA-L, comparative transcriptome analyses based on GS-FLX were conducted with total RNA extracted from CA-L, which generated ca. 143 Mb reads. Previously reported, comparative transcriptome analyses performed in imidacloprid resistant (CA-IR) and CA-S. The comparative transcriptome analyses re-investigated after all data sets were combined together. As previously reported, seven ATP-binding cassette (ABC) transporter genes were newly identified in A. gossypii, among which only ABCC9 gene was highly expressed in CA-IR and L. These results suggested that ABCC subfamily associated with imidacloprid resistance in A. gossypii.