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The free-living (FL) and particle-attached (PA) bacteria have different dispersal potentials and ecological roles in aquatic ecosystems. However, our knowledge of their diversity and regional biogeographic patterns in high-altitude alpine lakes is limited. In this study, to investigate the diversity and geographic patterns of the FL and PA bacterial communities and to quantify the relative influence of environmental filtering and dispersal limitation in shaping the FL and PA bacterial communities, we collected surface water samples from 26 lakes over 1000 kilometers on the Tibetan Plateau. The majority of sequences exclusively in the FL bacteria were Actinobacteria (29.4%), Proteobacteria (27.7%) and Bacteroidetes (21.6%), while sequences exclusively in the PA bacteria were dominated by Proteobacteria (57.9%). The alpha-diversity indices, including Shannon index and Pielou's evenness, were significantly lower in the FL bacteria than that in PA bacteria. The surrounding soils as an important potential source contributed more to the diversity of the PA bacteria than the FL bacteria. Both of the FL and PA bacterial communities exhibited a significant regional distance-decay pattern. Environmental filtering and dispersal limitation were significantly related to the spatial variation of the FL and PA bacterial communities, whereas the environmental filtering/dispersal limitation effect ratio was higher in the FL bacterial communities. Our study is the first to describe the regional-scale spatial variability and to identify the factors that drive regional variability of the FL and PA bacterial communities in Tibetan lakes.