Honey bee resistance to the parasitic tracheal mite Acarapis woodi is known to be mediated by autogrooming. During autogrooming, bees use their midlegs to remove migrating foundress mites, thereby reducing invasion into their tracheae. We investigated the relationship between markers identified by single nucleotide polymorphism association and variation in average colony infestation rates, and in individual bees from a backcrossed mapping population combining tracheal mite-resistant and susceptible lines. We identified a genetic interval that may confer resistance and postulate on potential candidate genes coded in the interval. Three genes, ionotropic glutamate receptor (iGluR), tyrosine hydroxylase (TyHyd), and Gemin3, are involved in primarily neural pathways and may impact autogrooming. However, inability to validate marker segregation with infestation phenotype in an unrelated population with clear but small differences in tracheal mite resistance shows that SNPs or other genetic markers cannot necessarily be presumed to be functional for marker-assisted selection.