We investigated bacterioplankton community structure in the southern East China Sea (ECS) based on pyrosequencing. In particular, we examined the relative contribution of local environmental conditions vs. dispersal processes in determining the spatial-temporal variation in community structure (relative abundance or presence/absence of taxa) of bacterioplankton. We analyzed the community as a whole as well as separating the data into four dominant taxonomic groups (Cyanobacteria, Alphaproteobacteria, Gammaproteobacteria and Actinobacteria). When considering presence/absence of species, we found local environmental effects in heterotrophic bacteria but not other groups. When considering relative abundance, no significant difference between environmental and dispersal effects was found for the community as a whole or heterotrophic bacteria. However, we found that Cyanobacteria community was better predicted by environmental factors while Alphaproteobacteria community was related to spatial predictors, i.e. dispersal constrain of Alphaproteobacteria was higher than that of Cyanobacteria. Contrary to the previous assertions that all bacteria have high dispersal capability and should be influenced by local environmental factors, these results suggested that different bacteria groups might have differential dispersal ability.