Acetaldehyde is oxidized from anaerobically accumulated ethanol during re-aeration in plants and may cause post-anoxic (post-hypoxic) injury. Aldehyde dehydrogenase (ALDH) can metabolize acetaldehyde to acetate, which is much less toxic. To understand the role of ALDH in alleviating post-anoxic injury of plants, we analyzed the expression of the mitochondrial ALDH genes, rf2a and rf2b, and determined the ethanol and acetaldehyde contents under submergence and subsequent re-aeration in a submergence-intolerant plant, maize (Zea mays L., inbred line B73). The level of rf2a mRNA decreased, whereas that of rf2b mRNA increased under submerged conditions. When the submerged plants were re-aerated, the transcript levels returned to the original levels. The level of mitochondrial ALDH proteins decreased under submergence and remained unchanged under re-aeration. The ALDH activity decreased under submergence and, during reaeration, recovered to the original level much more slowly than in the case of rice (Oryza sativa L.). The content of acetaldehyde, which was produced under submergence, further increased following re-aeration. These results suggest that the lower submergence tolerance of maize compared to that of rice is partly due to a weaker ALDH activity during re-aeration.