Taxodium ascendens and Quercus variabilis (Cork Oak) are very important species distributed in the subtropical riverside and drawdown area of reservoirs and ponds in China. In this study, to investigate the effects of waterlogging on the eco-physiological processes of these two species, the maximum net photosynthesis rate, apparent quantum yield（φ）, apparent carboxylation efficiency（CE）, content of soluble sugar of root/stem/leaf, Leaf Mass per unit Area (LMA) as well as the root activity of these two species under waterlogging conditions were measured. Waterlogging caused a persistent decrease of maximum photosynthetic rate of Cork Oak (on the 50th day of waterlogging, the value was only 9% of control). In contrast, there was no significant difference of maximum photosynthetic rate between waterlogged and control seedlings of Taxodium ascendens. It was shown that: (1) the φ of Cork Oak was decreased by waterlogging (6 days of waterlogging decreased φ to 59.9% of control, 26 days of waterlogging decreased φ to 40.9%), while waterlogging caused no significant change of φ of Taxodium ascendens; (2) under normal conditions, the CE of Cork Oak was approximately (0331±0.075)μmol m-2s-1Pa-1, waterlogging induced a persistent decrease of CE (10 days of waterlogging decreased CE to 221% of control, 30 days decreased to 16.8%), while waterlogging caused no significant changes in the CE of Taxodium ascendens;(3) the soluble sugar content of the root/stem/leaf of both species also showed kinetic responses under waterlogging stress. At the beginning of waterlogging (10th day), the soluble sugar content of the leaf and root of Cork Oak was less than the control; afterwards, it was higher than the control. Comparably, the soluble sugar content of stem of Cork Oak was higher than control during the period of treatment. As for Taxodium ascendens, the soluble sugar content of root/stem/leaf was not significantly different between waterlogging and control; (4) The LMA of waterlogged Cork Oak was higher than control, while there was no difference between control and treatment of Taxodium ascendens; (5) compared with control, the root activity of the waterlogged Cork Oak decreased persistently. While at early stage of waterlogging, the root activity of Taxodium ascendens was reduced to some degree; afterwards, it was higher than control, which might be due to the emergence of adventitious roots. The results above indicate that Cork Oak was more sensitive to waterlogging than Taxodium ascendens. This study indicates the underlying mechanisms contributing to the decreased photosynthesis rate of Cork Oak at the early stage of waterlogging, include the decreased apparent quantum yield and decreased apparent carboxylation efficiency. In addition, the feed-back effect of accumulated carbohydrates in leaves on the photosynthesis rate of Cork Oak may occur during long-term waterlogging.