Although the consequences of changes in microbial diversity have received increasing attention, our understanding of processes that drive spatial variation in microbial diversity remains limited. In this study, we sampled bacterial communities in early and late successional temperate forests in Northeast China, and used distance-based redundancy analysis to examine how different processes influence bacterial beta diversity and phylogeny-based beta diversity using the Bray–Curtis and UniFrac metrics, respectively. After controlling for sampling effects, bacterial beta diversity in both forests was higher than expected by chance, which indicates that the bacterial community showed strong intraspecific aggregation. Both environmental filtering and dispersal limitation contributed to bacterial beta diversity and phylogeny-based beta diversity in the two forests. However, the relative importance of these different processes varied between the two forests. In the early successional forest, dispersal limitation played a dominant role in structuring the bacterial community, whereas the effects of environmental filtering were more important in the late successional forest. Our study revealed that bacterial beta diversity and phylogeny-based beta diversity in forest communities from the same region are regulated by different forces and that the relative importance of different forces varies over succession.