Linkage of an acetylcholinesterase (AChE) gene was detected in the house fly, Musca domestica L., by using the backcross method between a strain, aabys, that had a morphological multichromosomal marker on each of the five autosomes and a wild strain, LPR. Both strains were homozygous in this gene, and we used eight single nucleotide polymorphisms (SNPs) between them to distinguish the parental sequences in the backcrossed progeny, two of which resulted in the amino acid substitiutions common to the Drosophila and Aedes AChEs insensitive to organophosphates and carbamates. F₁ appeared to be a wild phenotype, and the AChE gene was heterozyous of aabys and LPR. In the backcross progeny, 32 (2⁵) phenotypes appeared, and 10 phenotypes with one wild or morphological marker were picked up for genotyping by the SNPs of AChE gene. A combination of the morphological markers and the SNPs revealed that the AChE structural gene is linked to autosome 2 in the house fly.