The physiological responses of 2-year-old seedlings of Nuttalls oak (Quercus nuttalli) and Southern red oak (Q. falcata) with two treatments i.e., deep-drowning and shallow-drowning, were studied. Taxodium distichum was selected as a control. The survival rates of seedlings were calculated, the photosynthetic indices were detected by Licor-6400 photosynthetic system instrument,and the root activities of seedlings were tested by the method of triphenyltetrazolium chloride (TTC). Results showed that: 1) By experiencing flooding for 76 d and recovering for 60 d after water was drained off, all seedlings survived under the shallow-drowning treatment. None of Q. falcata seedlings died in the deep-drowning treatment until the 49th day. The survival rate of Q. falcata in the deep-drowning treatment was 30%. 2) Within 61 d of waterlogging treatments, the net photosynthetic rate (Pn), stomatal conductance (gs) and transpiration rate (Tr) showed a tendency of declining, but intercellular concentration of CO2 (Ci) increased. With the pro-longation of flooding stress, the extents of variation for all indices under deep-drowning treatment were larger than those under the shallow-drowning treatment. The variation of Q. falcata in flooding stress was larger than that of Q. nuttallii. 3) The root vigor and alcohol dehydrogenase (ADH) activities were detected at the 61st day in flooding stress. Waterlogging obviously inhibited root ac-tivities. Shallow-drowning made root vigor of Q. nuttallii decreased by 11.7%, and for Q. falcata, by 51.88%. Shallow-drowning treatment had no remarkable effects on ADH activities of seedlings, but deep-&owning increased those of Q. nuttallii seedlings by 227.24%, and decreased those of Q. falcata seedlings by 59.22% in the meantime. We conclude that Q. nuttallii had a stronger wa-terlogging resistance than Q. falcata, but weaker than T. distichum.