The water-level-fluctuation zone of the Three Gorges Reservoir was assumed to be completely formed in 2009 and the water level would range from 145 m in flood season (summer) to 175 m during non-flood season (winter). This hydrologic regime is the opposite of the Yangtze River's natural regime before the Three Gorges Dam construction when the peak flows occurred in summer and low flows occurred in winter. The reversal of flooding time, prolonged flooding duration will dramatically alter environmental conditions in the riparian zone. The fragility of the water-level-fluctuation zone has been widely recognized by Chinese scientific community and governments. It is common view that vegetation should give a priority for ecological restoration in the water-level fluctuation zone. Considering the special hydrological environment, annual plant species was assumed to be dominant component of the vegetation communities for their ability to fulfill their life history during the drawdown period. In order to select suitable annual plant resources for vegetation restoration, we examined the germination characteristics of fresh, cold stored and submerged (W 165-8 m, 121 d; W 155-18 m, 230 d; W 147-26 m, 271 d) seeds of nine annual plant species(Eclipta prostrate, Bidens pilosa, Artemisia annua, Aeschynomene indica, Digitaria sanguinalis, Echinochloa hispidula, Conyza canadensis, Bidens bipinnata, Setaria glauca), which growing in the Three Gorges Reservoir region. The submerged seeds were placed in the water-level-fluctuation zone of the Three Gorges Reservoir. The results indicated that effects of submergence in relation to fresh seeds on the germination percentage varied with the submergence conditions. In W 165 submergence treatment, germination percentages of seven species decreased significantly, and tow, E. hispidula and B. bipinnata had opposite trends. Germination percentages of six species decreased significantly, and three species germinated with low germination percentages 11.0%, 7.3% and 2.7% respectively in W 155. In W 147, germination percentages of E. hispidula and B. bipinnata also increased significantly, while germination percentages of E. prostrate showed no difference, and other species decreased significantly. No significant submergence effect was detected for D. sanguinalis, C. Canadensis and S. glauca, because they had very low germination percentages in all treatments. Seeds of E. prostrata, A. annua, B. bipinnata and E. hispidula demonstrated better tolerance to water submergence. In W 165 submergence treatment, their germination percentages were 44.7%, 42%, 20.7% and 4.3%, respectively. In W 147, germination percentages were 76.3%, 23%, 15% and 26.3%, respectively, and they were higher than other species. The temporal patterns of seed germination were also significantly influenced by submergence, manifesting in two ways, days to initial germination increased and the germination speed decreased for most of the species. It can be concluded that the seeds of E. prostrata, A. annua, B. bipinnata and E. hispidula are submergence-tolerant, and the plants are able to accomplish their life history during the drawdown period. The result of this experiment suggests great potential of annual plant species in vegetation restoration of water-level-fluctuation zone in the Three Gorges Reservoir. And we should apply them according their different biological characters. E. prostrate and E. hispidula can be used at the lower elevations of water-level-fluctuation zone while A. annua and B. bipinnata should be planted at the upper elevations.