Abstract:[Objective] We compared the difference of community structure of archaea between Qinghai Lake (the largest inland saltwater lake in China) and several other salt lakes in China.[Methods] Chaka Salt Lake in Qinghai Province, Huamachi Salt Lake and Gouchi Salt Lake in Shaanxi Province, and Yuncheng Salt Lake in Shanxi Province were randomly selected as the sample pool. From each lake five samples were taken and analyzed with the high-throughput sequencing technology for 16S rRNA gene.[Results] The dominant genera of Qinghai Lake were DHVEG-6_norank, Methanomicrobia_unclassified, Methanobacterium, Methanolobus, Candidatus_Methanomethylophilus, Miscellaneous_Euryarchaeotic_Group(MEG)_norank, AMOS1A-4113-D04_norank, Methanosarcina, Miscellaneous_Crenarchaeotic_Group_norank. Among them DHVEG-6_norank (70.46%) was absolutely dominant whereas it was hardly found in other salt lakes. On the contrary, the dominant genera in the other 4 salt lakes are Halonotius, Halorubrum, Natronomonas, Halobellus and Haloarcula. Degree of mineralization was the most influential factor that affected the structure of the archaea communities in Qinghai Lake and other salt lakes. The community structure of Qinghai Lake with a low degree of mineralization was significantly different from that of the other 4 salt lakes. The second factor is pH that affected the abundance of some species. However, no significant correlation between the altitude and the community structure was found.[Conclusion] The community structure and diversity of Qinghai Lake was significantly different from that of other 4 salt lakes and it was mainly influenced by the degree of mineralization.