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Puma Yumco Lake (PYL) is an ultraoligotrophic freshwater lake that sits an altitude of 5030 m within the Qinghai-Tibet Plateau of China. The bacterial and archaeal diversity of the lake remains poorly understood, despite their potential to inform on biogeochemical cycling and environment-microbial associations in these unique environments. Here, the bacterial and archaeal communities of PYL were investigated using high-throughput sequencing analysis of community 16S rRNA gene sequences. Further, the relationships among dominant taxa and environmental factors were comprehensively evaluated. Bacterial diversity comprised 31 phyla and 371 genera (10,645 operational taxonomic units [OTUs], Shannon index values of 5.21–6.16) and was significantly higher than that of Archaea (five phyla and 24 genera comprising 1141 OTUs and Shannon index values of 1.18–3.28). The bacterial communities were dominated by Proteobacteria (48.42–59.97% relative abundances), followed by Bacteroidetes (12.5–32.51%), Acidobacteria (2.07–11.56%), Firmicutes (0.65–6.32%), Planctomycetes (0.99–3.56%), Gemmatimonadetes (0.38–3.57%), Actinobacteria (1.67–3.52%), Verrucomicrobia (0.87–2.01%), and Chloroflexi (0.5–1.17%). In addition, archaeal communities were dominated by Thaumarchaeota (33.22–93.00%), followed by Euryarchaeota (2.89–35.47%), Woesearchaeota (0.99–31.04%), and Pacearchaeota (0.01–1.14%). The most abundant bacterial genus was Rhodoferax (5.73–26.62%) and the most abundant archaeal genus was the ammonia-oxidizing Nitrososphaera (29.18–91.46%). These results suggest that the Rhodoferax and Nitrososphaera are likely to participate in biogeochemical cycles in these environments through photoheterotrophy and nitrification, respectively. Taken together, these results provide valuable data for better understanding microbial interactions with each other and with these unique environments. [ABSTRACT FROM AUTHOR]