Taking Meizao/Dongbeishanyingtao (Prunus serrulata G. Don) and Meizao/Mahaleb (P. mahaleb L.) as test materials, the respiration intensity and respiratory enzyme activities of their growing roots and brown lignified roots were determined under waterlogging. The results showed that under waterlogging, the root respiration intensity of the two kind rootstocks had a decreasing trend, with more decrement for their growing roots. For P. serrulata, the decrement of the respiration intensity of its growing roots and brown lignified roots was 1.47 and 1.36 times as much as that of P. mahaleb, respectively. The pyruvate decarboxylase (PDC) and lactate dehydrogenase (LDH) activities of the two kind roots had a decrease after an initial increase. Alcohol dehydrogenase (ADH) activity in growing roots also had a decrease after an initial increase, but that in brown lignified roots had an increasing trend. The test three enzyme activities changed more in growing roots than in brown lignified roots. The increment of ADH and LDH activities was higher for P. serrulata than for P. mahaleb, while PDC activity was in adverse. The malate dehydrogenase (MDH) activity of the two kind roots decreased, and the decrement was larger in growing roots than in brown lignified roots. P. serrulata had a larger decrement of root MDH activity than P. mahaleb To the waterlogging stress, growing roots was more sensitive than brown lignified roots, and P. serrulata was more sensitive than P. mahaleb.