We previously found that malathion residue in wheat kernels was decomposed by wheat kernel carboxylesterase (CE) during sample preparation for pesticide residue analysis. The degradation of malathion in supernatant of wheat kernel homogenate was enzyme-kinetically analyzed to characterize the CE. Malathion α-monocarboxylic acid (MMCα), malathion β-monocarboxylic acid (MMCβ), malathion dicarboxylic acid (MDC) and desmethyl malathion (DMal) were identified by analysis using liquid chromatography/electrospray ionization mass spectrometry (LC/ESI-MS) after incubation at 36• C of the reaction mixture of malathion in the supernatant of wheat kernel homogenate. Since small amounts of DMal and MMCβ were formed in boiled supernatant of wheat kernel homogenate, these compounds were nonenzymatically produced. Examination of the time course of enzymatic malathion degradation indicated that malathion was decomposed into MDC through both MMCα and MMCβ, and the amount of MMCα formed was greater than that of MMCβ at maximum concentrations of both MMC isomers. MMCα and MMCβ were enzymatically decomposed into only MDC, which was the final metabolite of malathion because there was no further decomposition product. The order of degradation half-lives by wheat kernel CE (malathion < MMCβ < MMCα) is consistent with the intensity of their hydrophobicity. These results suggest that when malathion is degraded via MMC to MDC by wheat kernel CE, its enzymatic degradability and the decomposition products depends on their hydrophobicity.