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Hydrological alternation can dramatically influence riparian environments and shape riparian vegetation zonation. However, it was difficult to predict the status in the drawdown area of the Three Gorges Reservoir (TGR), because the hydrological regime created by the dam involves both short periods of summer flooding and long-term winter impoundment for half a year. In order to examine the effects of hydrological alternation on plant diversity and biomass in the drawdown area of TGR, twelve sites distributed along the length of the drawdown area of TGR were chosen to explore the lateral pattern of plant diversity and above-ground biomass at the ends of growing seasons in 2009 and 2010. We recorded 175 vascular plant species in 2009 and 127 in 2010, indicating that a significant loss of vascular flora in the drawdown area of TGR resulted from the new hydrological regimes. Cynodon dactylon and Cyperus rotundus had high tolerance to short periods of summer flooding and long-term winter flooding. Almost half of the remnant species were annuals. Species richness, Shannon-Wiener Index and above-ground biomass of vegetation exhibited an increasing pattern along the elevation gradient, being greater at higher elevations subjected to lower submergence stress. Plant diversity, above-ground biomass and species distribution were significantly influenced by the duration of submergence relative to elevation in both summer and previous winter. Several million tonnes of vegetation would be accumulated on the drawdown area of TGR in every summer and some adverse environmental problems may be introduced when it was submerged in winter. We conclude that vascular flora biodiversity in the drawdown area of TGR has dramatically declined after the impoundment to full capacity. The new hydrological condition, characterized by long-term winter flooding and short periods of summer flooding, determined vegetation biodiversity and above-ground biomass patterns along the elevation gradient in the drawdown area. [ABSTRACT FROM AUTHOR]