The complete coding sequences of two acetylcholinesterase (AChE) genes, Ace1 (orthologous to Drosophila Ace) and Ace2 (paralogous to Ace), from the cotton aphid (Aphis gossypii) were identified and sequences from carbamate resistant and susceptible strains compared. No change in the amino acid sequences was found in Ace1, while two amino acid substitutions, Ser431Phe and Ala302Ser, were detected between resistant and susceptible strains in Ace2. The position of Ser431Phe corresponds to one of fourteen aromatic residues lining the active site gorge and is located in the acyl pocket. Ala302Ser is located at one of the three residues which form the oxyanion hole in the active site of AChE. The Ser431Phe and Ala302Ser substitutions may play a role in pirimicarb and organophosphate resistance, respectively.