Seed bank composition and germination characteristics are necessary for modeling wetland vegetation composition. Yet there are few studies about the seed bank difference between plant communities in lakeshore wetlands. Seed banks are also known to play important roles in the vegetation restoration process. Environmental factors such as water level, temperature, or nutrient levels can affect vegetation composition and seed bank composition. The relationships between environmental factors and seed banks of wetlands in the field are still unknown. The Jiuzhaigou Nature Reserve is located at the eastern edge of Qinghai-Xizang Plateau. The lakeshore wetland vegetation is dominated by Phragmites australis (Cav.)Trin. ex Steud., Typha latifolia L., Carex pamirensis C. B. Clarke, Equisetum fluviatile L. The wetlands in Jiuzhaigou (118 lakes) are under strong pressure such as trampling and enhanced construction for travel. Plant restoration is necessary for protection of these areas. We investigated the soil seed bank in six lakeshore wetlands in this area using the seedling emergence method. Sediment samples (0-2 cm, 2-5 cm, 5-10 cm intervals from surface to bottom) were taken with core (diameter 5 cm) in April and from each replicate samples were spread on two plastic trays. Trays were randomly arranged in the greenhouse and watered daily. Seedlings were counted weekly after emergence, and removed as soon as they could be identified. Our study showed that seed density in all soil layers samples was negatively correlated to water depth. Water depth can explain 45% variance of species richness in surface layer in sediment. Species richness in extant vegetation can explain 45, 48, 25% variance of species richness in total 10 cm and in 2-5 cm and 5-10 cm layer sediment respectively. Dominant species cover in extant vegetation, site altitude, total nitrogen, total phosphorus and total organic carbon in soil showed no correlation with species richness in seed bank. Mean seed densities in wetlands ranged from 0 to 15945 m[^-2]. A total of 23 species germinated in seed bank, while 85 species were found in extant vegetation. The dominant species in seed bank and extant vegetation showed great difference. The total number of species and seedlings that germinated in different layers was not significantly different. But the second layer had the greatest seed density. The relationship between seed bank and extant vegetation differed from one species to another. We should use different restoration strategies for different plant communities.