Primary structural information of a plant aldehyde oxidase (AO), which was purified from maize coleoptiles using indole-3-acetaldehyde as a substrate, was obtained by sequencing a series of cleavage peptides, permitting the cloning of the corresponding cDNA (zmAO-1). The complete nucleotide sequence was determined; the deduced amino acid sequence encodes a protein of 1358 amino acid residues of Mr 146,681, which is consistent with the size of the AO monomeric subunit. There is a significant similarity with AO from mammals and xanthine dehydrogenases from various sources. The maize AO polypeptide contains consensus sequences for iron-sulfur centers and a putative molybdopterin cofactor-binding domain. In addition, another cDNA (zmAO-2), highly homologous to zmAO-1 at both the nucleotide and amino acid sequence levels, was cloned. zmAO-2 would encode a protein of 1349 amino acid residues of Mr 145,173 and has molecular characteristics similar to those of zmAO-1. zmAO-1 was expressed at a high level in roots, which was closely correlated with immunoblotting results using antiserum raised against the purified maize AO protein, whereas zmAO-2 was expressed at a higher level in coleoptiles than in roots. We propose each zmAO may have a unique function during plant development.