Meizao/Dongbeishanyingtao(Peunus serrulata G. Don) and Meizao/Mahaleb (Prunus mohaleb L.) were chosen as experiment materials. The activities of anaerobic respiration enzymes including pyruvate decarboxylase(PDC), alcohol dehydrogenase(ADH) and lactate dehydrogenase(LDH) in both sweet cherry rootstock growing roots and brown lignified roots as well as the contents of the fermentation products including acetaldehyde, ethanol and lactate in the brown lignified roots were studied under water-logging. The results showed that the PDC and LDH activities increased at first and then decreased in both kinds of roots, so the ADH activity in growing roots did, but the ADH activity in brown lignified roots increased. These enzyme activities in growing roots changed much more than those in brown lignified roots. The ADH and LDH activities in both Meizao/Dongbeishanyingtao roots increased much more than that of Meizao/Mahaleb roots, but PDC reversed. The contents of acetaldehyde and ethanol increased in both brown lignified roots, however, lactate increased at first and then decreased. At last the acetaldehyde content in brown lignified roots of Meizao/Dongbeishanyingtao was lower than Meizao/Mahaleb, but the ethanol content reversed, as for lactate, the former maximum was higher than the latter and reached the maximum earlier.