We examined species composition and richness in the seed banks and established vegetation in lakes along the Yangtze River with two contrasting aquaculture types: pen-culture lakes, characterized by pen-culture of commercial fish and crab, and lake-culture lake with more intensive stocking of the entire lake. The mean live biomass and species richness of submerged vegetation was significantly reduced or absent in lake-culture lakes (0–159gm^？2 and 0–0.3 species per sample, respectively), compared to those with pen-culture lakes (1552–2971gm^？2 and 1.5–3.2 species per sample, respectively) in all three study years. Also mean seedling density and species richness of seed banks were significantly lower in these lake-culture lakes (133m^？2 vs. 265m^？2 and 0.6 species vs. 0.9 species per sample, respectively). These results suggest that intensive aquaculture in these lakes has had serious negative effects on submerged vegetation and the associated seed banks. Vegetation history was partly reflected by distribution patterns of seed banks across sediment depth strata. A principal component analysis produced a very clear separation of lakes from pen-culture and lake-culture on the basis of their species composition. Moreover, the principal component analysis also indicated that the variation in the soil seed bank corresponded poorly with vegetation data. This probably reflects species-specific strategies for seed production.