Thousands of hot springs are located in the north-eastern part of the Yunnan–Tibet geothermal zone, which is one of the most active geothermal areas in the world. However, a comprehensive and detailed understanding of microbial diversity in these hot springs is still lacking. In this study, bacterial and archaeal diversities were investigated in 16 hot springs (pH 3.2–8.6; temperature 47–96°C) in Yunnan Province and Tibet, China by using a barcoded 16S rRNA gene-pyrosequencing approach.Aquificae,Proteobacteria,Firmicutes,Deinococcus-ThermusandBacteroidetescomprised the large portion of the bacterial communities in acidic hot springs. Non-acidic hot springs harboured more and variable bacterial phyla than acidic springs.Desulfurococcalesand unclassifiedCrenarchaeotawere the dominated groups in archaeal populations from most of the non-acidic hot springs; whereas, the archaeal community structure in acidic hot springs was simpler and characterized bySulfolobalesandThermoplasmata. The phylogenetic analyses showed thatAquificaeandCrenarchaeotawere predominant in the investigated springs and possessed many phylogenetic lineages that have never been detected in other hot springs in the world. Thus findings from this study significantly improve our understanding of microbial diversity in terrestrial hot springs.