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The Salar de Uyuni, situated in the Southwest of the Bolivian altiplano, is the largest salt flat on earth. Brines of the athalassohaline hypersaline environment are rich in lithium and boron. Due to the ever-increasing commodity demand the exploitation of brines for metal recovery from the world's largest lithium reservoir is likely to increase substantially in the near future. Only few studies have investigated the composition of halophilic microbial communities in brine waters of the Salar. Here we report on the microbial diversity of brine pools in the East, locally denoted "Ojos del Salar". The brine is characterized by a salinity of 28%, slightly acidic pH and high lithium concentrations. Four pool communities were analysed by sequencing the V3-V4 region employing Illumina MiSeq technology. Subsequently, Mothur was used for sequence processing and data analysis. Metagenomic analysis revealed the occurrence of an exclusively archaeal community comprising 24 halobacterial genera including only recently identified genera like Halapricum, Halorubellus and Salinarchaeum. Despite the high diversity of the encountered halobacteria community, almost half of the Halobacteria assigned sequences (46%) could not be classified on the genus level under stringent filtering conditions. Thus, it seems likely to discover new, hitherto undescribed genera in this particular habitat of Salar de Uyuni. [ABSTRACT FROM AUTHOR]