Abstract:[Objective]We characterized procaryotic biodiversity,community structure and the relationship between the community structure and environmental factors of salt lakes in Badain Jaran desert,Inner Mongolia,China.[Methods]We constructed 16S rRNA gene clone libraries by molecular biology techniques to analyze the procaryotic phylogenetic relationships,and used R language to compare the community structure of haloalkalophiles in the salt lakes.[Results]Water in this region has a high salinity ranging from 165 to 397 g/L.The water is strongly alkaline with pH value above 10. The microbial diversity and community structure of the salt lakes are obviously different. The diversity of bacteria is more abundant than that of archaea.The main categories of bacteria in the samples are Gammaproteobacteria,Bacteroidetes,Alphaproteobacteria,Firmicute and Verrucomicrobia,whereas all archaea only belong to Halobacteriaceae of Euryarchaeota.[Conclusion]Salinity is the most important environmental factor influencing the bacterial community structure,whereas the archaea community structure was influenced comprehensively by multiple environmental factors.