[Background] Rehai hot springs in Yunnan Province contain a wealth of extreme microbial resources. [Objective] This study was proposed to study the microbial diversity and community structures in Rehai hot springs, especially the diversity of iron- and sulfur-oxidizing microorganisms in the acid hot springs. [Methods] The microbial 16S rRNA V4?V5 genes region was sequenced by Illumina HiSeq technology and analyzed by bioinformatics software. [Results] A total of 578 061 high-quality sequences were obtained from 15 samples of 3 hot springs, resulting in 141 OTU belonging to 19 phyla, 66 genera. Crenarchaeota and Firmicutes were main phyla in Gumingquan (GMQ), Hamazui (HMZ) and Huangguaqing (HGQ). On the genera level, there were 37 and 32 genera in alkaline hot spring GMQ and neutral hot spring HMZ, respectively, in which the major genera were Bacillus and Pyrobaculum. Among the 20 genera present in acidic hot spring HGQ, the genera Acidibacillus and Acidithiobacillus were dominant. Furthermore, some species of Acidicaldus, Sulfobacillus, Sulfolobus and Metallosphaera genera were isolated from HGQ, which have potential to oxidize iron and sulfur. [Conclusion] The microbial resources were diverse in Rehai hot springs and the microbial compositions of the three hot springs were obviously different. Iron- and sulfur-oxidizing microorganisms, uncultured and unclassified microbes, especially archaea, were rich in acidic HGQ.