Abstract: High survival rate of long-term flooding was observed in Arundinella anomala and Salix variegata, two riparian plant species in the Yangtze River water fluctuation zone. Survival of flooding is supposed to be associated with carbohydrate utilization. Survival rate and carbohydrate (soluble sugar and starch) concentration of these two plants were investigated in a simulated flooding experiment lasting up to six months. Three water level treatments (waterlogging, 2 m deep water submergence, and non-flooded control) and four flooding durations (40, 90, 120 and 180 days) were set. Plants death only occurred to A. anomala after 120 days and S. variegata after 180 days which were submerged in 2 m deep water, while all the waterlogged plants of both species survived after 180 days. Carbon storage was found mainly in stems of A. anomala and stems and coarse roots of S. variegata plants. Carbohydrate concentration was very low in roots of A. anomala and in fine roots of S. variegata plants. Waterlogging slightly decreased biomass production and soluble sugar and total starch concentration compared with non-flooded plants. In contrast, 2 m submergence treatments lead to a gradually decrease in biomass while a sharp decrease in soluble sugar and starch concentration in all tissues within 90 days in both species; and then the carbohydrate mobilization slowed down. The results suggested that mortality of long-term submergence might be caused by disabled carbon storage mobilization in the later stages of prolonged flooding. The high flooding tolerance in the two species can be explained by the ability to mobilize carbohydrate storage in the beginning and later when exposed to carbon starvation. Differences of the responses to flooding between A. anomala and S. variegata could be ascribed to their different carbohydrate storage distribution patterns.