We applied under pot-culture conditions and the double-casing pot method to study the characteristics of photosynthetic gas exchange and chlorophyll fluorescence in the leaves of Physocarpus amurensis Maxim (PA) and Physocarpus opulifolius under flooding stress. Our results indicate a significantly higher flooding tolerance of P. opulifolius compared to P. amurensis. Especially in P. amurensis, the limitation of non-stomatal factors played a major role in the advanced stages of flooding stress, observed as a rapid increase of the intercellular CO2 concentration (C i) and a decrease of the stomatal limitation value (L s). The maximal PSII photochemical efficiencies (F v/F m) and actual photochemical efficiency (Ф PSII) in the leaves of P. opulifolius were significantly higher, and the extent of decrease during the flooding process was smaller than in P. amurensis. In addition, the non-chemical quenching (NPQ) in the leaves of P. opulifolius significantly increased from the 10th day under flooding stress, while the variation of NPQ in the leaves of P. amurensis was much smaller. This indicates that the leaves of P. opulifolius had not only higher PSII photochemical activity, but also improved tolerance to flooding stress, which may be caused by its ability to dissipate excess excitation energy by starting NPQ. At the 16th day under flooding stress, the P IABS significantly decreased with greater extent of decrease than F v/F m in the leaves of both Physocarpus, but the decreasing extent of P IABS in P. opulifolius was significantly smaller than in P. amurensis. In the 16th day under flooding stress, the fluorescence at J and I point (V J and V I) in P. amurensis were significantly higher, and the extent of increase in V J was greater than V I. However, the variations of V J and V I in the leaves of P. opulifolius were smaller, suggesting that the damage sites of flooding stress to PSII in the leaves of P. amurensis were mainly located in the electron transport process from QA at the PSII receptor side to QB. Flooding stress reduced the proportion (φE o ) of luminous energy absorbed by the PSII reaction center for the electron transport following Q A − , while the maximum quantum yield (φD o) of non-photochemical quenching increased. However, the TRo/RC and ETo/RC in the leaves of P. amurensis decreased accompanied by a dramatic increase of energy (DIo/RC) from the dissipation in the reaction center. This further indicated that the function of the PSII reaction center in the leaves of P. amurensis was significantly lower than in P. opulifolius.