Abstract:[Background] The microbial communities in desert lakes have unique structures, which are crucial for maintaining the ecological balance and improving the biodiversity in deserts. [Objective] To explore the relationship between archaeal community structures and environmental factors in salt lakes of Badain Jaran Desert. [Methods] The 16S rRNA gene amplicon sequencing and bioinformatics were employed to analyze the distribution, diversity, and structures of archaeal communities in six salt lakes of Badain Jaran Desert. The Pearson correlation analysis, Mantel test, and redundancy analysis (RDA) were performed to explore the effects of environmental factors on archaeal community structures. [Results] Piper diagram showed that the six lakes were all salt lakes of the Na+-Cl--CO32- type. The fitting analysis showed that the Simpson index, Shannon index, and Pielou index of the archaeal community had linearly positive correlations with salinity. The archaea in salt lakes belonged to 59 genera, 38 families, 25 orders, 17 classes of 11 phyla, among which Halobacteriota was absolutely dominant with the relative abundance of 99%. Halorubrum was the dominant genus shared by the six salt lakes, and there were still a large number of unclassified genera. The correlation analysis showed that pH, Cl-, CO32-,and K+significantly affected the alpha diversity of archaeal communities. The Mantel test showed that pH, CO32-, Cl-, and K+ were important environmental factors affecting archaeal genera. The results of RDA showed that CO32- significantly influenced the archaeal community. [Conclusion] The diversity of archaeal communities in different salt lakes of Badain Jaran Desert is positively correlated with salinity, and the archaeal communities in salt lakes are mainly affected by pH, CO32-, Cl-, and K+. In addition, there are abundant unclassified archaeal genera, which indicate the existence of abundant new species resources.