Toxin-binding proteins of insect midgut epithelial cells are associated with insect resistance to Bacillus thuringiensis (Bt) Cry toxins. A 5378 nt cDNA encoding a 1717 amino acid putative midgut cadherin-like glycoprotein and candidate Cry1Ab toxin-binding protein was characterized from Ostrinia nubilalis. Intraspecific alignment of partial O. nubilalis cadherin gene sequences identified variance within proposed Cry1A toxin binding region 2 (TBR2), 1328IPLQTSILVVT[I/V] N1340, and flanking Cry1A toxin binding region 1 (TBR1), 861DIEIEIIDTNN871. DNA sequence and PCR-RFLP detected single nucleotide polymorphism between cadherin alleles, and pedigree analysis demonstrated Mendelian inheritance. A population sample from Mead, Nebraska showed allelic polymorphism. These assays may be useful for linkage mapping and field surveillance of wild populations and of O. nubilalis.