The Tibetan Plateau, also termed ‘the Third Pole’ harbors the largest number of high-altitude lakes in the world. Due to the presence of extreme conditions such as low temperature and oligotrophy, the lakes of the Tibetan Plateau share environmental features in common with lakes in the polar regions. However, the extent to which these environments are analogous, or indeed whether they harbor similar microbial communities or a high level of endemic species is poorly understood. Here we compared high-throughput 16S rRNA gene sequencing data from the lakes of the three different regions in order to characterize their taxonomic diversity, the community composition and biogeography. Our results showed despite the similarity in environmental conditions, the spatial distribution of the bacterial communities was distinct with only 3.1% of all operational taxonomic units (OTUs) being present in all three regions (although these OTUs did account for a considerable proportion of the total sequences, 36.4%). Sequences belonging to Burkholderiales and Actinomycetales dominated the shared OTUs across all three regions. Scale dependent distance decay patterns provided evidence of dispersal limitation. Climatic variables and dispersal limitation were apparently both important in controlling the spatial distribution of bacterial communities across regions. This work expands our understanding of the diversity and biogeography of lake bacterial communities across the Tibetan Plateau and provides insights into how they compare to those of the Antarctic and Arctic.