The Rehai and Ruidian geothermal fields, located in Tengchong County in Yunnan Province, China, host a variety of geochemically distinct hot springs. In this study, we report a comprehensive, cultivation-independent census of microbial communities in 37 samples collected from these geothermal fields, encompassing sites ranging in temperature from 55.1 to 93.6 oC and in pH from 2.5 to 9.4. Richness was low in all samples, with 21-123 species-level OTUs detected. The bacterial phylum Aquificae or archaeal phylum Crenarchaeota were dominant in all samples from Rehai, yet the dominant taxa within those phyla depended on temperature and pH. Low pH (2.5-2.6) and high temperature (85.1-89.1°C) favored the crenarchaeal order Sulfolobales, whereas low pH (2.6-4.8) and cooler temperature (55.1-64.5 °C) favored the Aquificae genus Hydrogenobaculum. Neutral to alkaline pH (7.2-9.4) favored the Aquificae genus Hydrogenobacter and crenarchaeal orders Desulfurococcales and Thermoproteales. Ruidian water samples harbored single predominant Aquificae genus Hydrogenobacter , whereas sediment samples from Ruidian were more diverse at the phylum level, with a higher abundance of yet uncultivated lineages and close relatives of the ammonia-oxidizing archaeon “Candidatus Nitrosocaldus yellowstonii”. The results of this study significantly expand the current understanding of the microbiology in Tengchong hot springs and provide a basis for comparison with other geothermal systems around the world.