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Although previous studies have compared the diversity and community composition of free-living (FL) and particle-attached (PA) bacterial groups in marine ecosystems, few studies have focused on the FL and PA bacterial communities in large and shallow eutrophic lakes. Furthermore, the assembly processes of the FL and PA bacterial communities have not been investigated. To illustrate the differences between PA (≥5.0 μm) and FL (0.22-5.0 μm) bacterial communities, samples were collected from 13 different sites in Taihu Lake, China. A higher diversity of the PA bacterial group than that of the FL group was observed, and significant differences in bacterial community composition between FL and PA groups were found (analysis of similarity, R = 0.2425, P < 0.001). Moreover, the two groups exhibited different relationships with environmental factors and geographic distance. Environmental factors played more important roles in affecting the FL bacterial community. A deterministic process was found as the primary factor driving the community of FL bacteria in Taihu Lake. However, the PA bacterial group was characterized by insignificant results of partial Mantel tests, which indicated that the community assembly was controlled by unknown processes.