Abstract:The effects of flooding depth on gas exchange, chlorophyll fluorescence and growth of Melaleuca alternifolia seedlings were studied. Seedlings were subjected to two hydrological treatments: shallow flooding and deep flooding with water level at 5cm and 20cm above the soil surface, respectively. Results indicated that the effect of flooding on Melaleuca alternifolia was elevated with the increase in the flooding depth. After 270 days of flooding, the height and biomass of the shallow-flooded and deep-flooded seedlings were significantly lower, accounting for 90.86%, 64.58% and 74.52%, 3646% of the control, respectively. Chlorophyll content, net photosynthetic rate, stomatal conductance and transpiration rate of the shallow-flooded seedlings were all slightly lower, accounting for 95.39%, 94.26%, 90.02% and 88.94% of the control, respectively. However, these parameters in the deep-flooded seedlings were all significantly lower within 180 days of flooding, accounting for 79.44%、73.54%、61.79% and 71.46% of the control, respectively, and then approached gradually to those of the control. There were no differences in the maximum quantum efficiency of the photosystemⅡ(Fv/Fm) between the shallow-flooded and control seedlings. Fv/Fm of the deep-flooded seedlings was slightly lower within 150 days of flooding, and then recovered to the levels of the control. A slight reduction of photochemical quenching coefficient (qP) and an increase of non-photochemical quenching (NPQ) in the shallow-flooded seedlings were observed, accounting for 96.63% and 105.66% of the control, respectively. However, a pronounced decrease of qP and an increase of NPQ in the deep-flooded seedlings were found within 120 days of flooding, accounting for 94.51% and 126.66% of the control, respectively, and then approached gradually to those of the control. Moreover, M. alternifolia developed aerenchyma and adventitious roots during inundation, with root porosity in the flooded seedlings much higher than that of the control.