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Greenland and the Tibetan Plateau, also known as the third pole, are both cold environments where anthropogenic activities are relatively weak. There are multitudinous lakes in both regions, especially in Greenland, where small water bodies are continuously created as glaciers retreat. It is unclear whether the community structure and community assembly mechanisms of these water bodies are consistent with those of lakes in the Tibetan Plateau that were indirectly influenced by glaciers. In addition, due to different evolution times of the lakes, differences of microbial diversity, especially at the sub‐species level, are feasible but not yet reported. Microbial compositions in lake water and sediment were investigated based on high‐throughput sequencing of 16S rRNA genes. The oligotyping analysis revealed disproportionally distributed bacterial oligotypes in lakes between the two different areas. Moreover, microbial macrodiversity and intra‐operational taxonomic units microdiversity is significantly higher in Greenland lakes which experiencing early lake ontogeny. Microbial community composition and functionality significantly distinguished between the two regions and habitats. Multivariate analysis together with null model tests demonstrated that deterministic processes largely controlled the patterns of community structure in the sediment, while stochastic processes are more important for those in pelagic water in both regions. Microbes may be further subject to N and P co‐limitation in line with the evolution of lake ecosystems. The obtained results could help us understand evolution trajectory of these polar lakes under the future climate change scenario.