The cotton aphid, Aphis gossypii Glover (Hemiptera: Aphididae), is a highly polyphagous pest that inflicts serious damage to a broad range of agricultural, horticultural and greenhouse crops. In Australia, A. gossypii is a significant pest of cotton and is difficult to control with insecticides because of its high propensity to develop resistance. Neonicotinoids are among the most effective insecticides used to control A. gossypii but the most recent detection of resistance threatens their longevity. Consequently, I aimed to restore neonicotinoid efficacy against A. gossypii through elucidation of underlying resistance mechanism(s). Bioassay was used to measure thiamethoxam (neonicotinoid) response in three field strains collected from commercial cotton. A second trial investigated the use of phorate (an organophosphate) as an alternative pre-germination treatment to thiamethoxam. PCR-Sequencing was employed to identify if mutation R81T known to confer resistance to neonicotinoid compounds was present in Australian A. gossypii. High-throughput sequencing of the A. gossypii transcriptome found differences in gene expression associated wit hthiamethoxam resistance. Two transcripts involved in the detoxification of xenobiotics (putatively annotated as cytochrome p450 gene 6K1-like) were found differentially expressed between resistant and suceptible strains. Transcript expression was further validated by qRT-PCR and showed a similar tendency in upregulation of expression. As such I identified this gene as the strongest candidate for thiamethoxam resistant A. gossypii. This study has generated a comprehensive transcriptome resource for A. gossypii that has characterised the expression of numerous important transcripts encoding proteins involved in insecticide resistance. Consequently, my study will contribute to future research relating to molecular characterization of insecticide resistance mechanisms in A. gossypii and other insect pests.