Responses of bald cypress (Taxodium distichum) and pond cypress (Taxodium ascendens) saplings in photosynthesis and growth to long-term periodic submergence in situ in the hydro-fluctuation zone of the Three Gorges Dam Reservoir (TGDR) were studied. Water treatments of periodic deep submergence (DS) and moderate submergence (MS) in situ were imposed on 2-year-old bald cypress and pond cypress saplings. The effects of periodic submergence on photosynthesis and growth were investigated after 3 years (i.e. 3 cycles) compared to a control (i.e. shallow submergence, abbreviated as SS). Results showed that pond cypress had no significant change in net photosynthetic rate (Pn) in response to periodic moderate and deep submergence in contrast to a significant decrease in Pn of bald cypress under both submergence treatments, when compared to that of SS. Ratios of Chlorophyll a/b and Chlorophylls/Carotenoid of pond cypress were significantly increased in periodic moderate submergence and deep submergence, while bald cypress showed no significant change. Diameter at breast height (DBH) and tree height of both species were significantly reduced along with submergence depth. Relative diameter and height growth rates of the two species were also reduced under deeper submergence. Moreover, bald cypress displayed higher relative diameter growth rate than pond cypress under deep submergence mainly attributed to higher productivity of the larger crown area of bald cypress. When subjected to deep subergence, both species showed significant reduction in primary branch number, while in moderate submergence, bald cypress but not pond cypress showed significant reduction in primary branch number. These results indicate that both bald cypress and pond cypress are suitbale candidates for reforestation in the TGDR region thanks to their submergence tolerance characteristics, but bald cypress can grow better than pond cypress under deep submergence overall.