The cDNA fragments of a 2kb gene, encoding the housefly acetylcholinesterase (AChE) were compared among 6 strains. While there were 4 substitutions of amino acids in the predicted peptides between Asp(83) and Arg(648), which is well conserved in insects, the following contrasts were made among the strains. The insecticide susceptible strains, aabys and SRS had Gly(342) and Phe(407), and the resistant strains, LPR, YBOL and YPRN had Ala(342) and Tyr(407), with Val(342) unique to YBOL. In addition, Leu(260) was found only in the chiral organophosphate resistant strains, YBOL and YPRN. These results showed that the patterns of single nucleotide polymorphisms, which resulted in amino acid substitutions, can be a practical tool for characterization of the insecticide resistance of houseflies.