The Aphis gossypii clone, Kushima, which was first discovered in Miyazaki Prefecture, Japan, exhibits significant resistance to neonicotinoid insecticides. We investigated the resistance mechanism involved by sequencing the nicotinic acetylcholine receptor (nAChR) gene, by electrophysiological analysis, and by insecticidal tests in the presence or absence of the oxidase inhibitor, piperonyl butoxide. The Kushima clone showed higher resistance to nitro-substituted neonicotinoids, such as imidacloprid, than to cyano-substituted neonicotinoids, such as acetamiprid. Sequencing of the nAChR subunit genes of a susceptible clone and the Kushima clone revealed an R81T mutation in loop D of the β1 subunit in the resistant clone. This mutation led to a significant shift in the pEC 50 value of imidacloprid for the Drosophila melanogaster Dα2-chicken β2 subunit, while it barely affected the concentration-response curves of acetylcholine and acetamiprid.