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The Dong Taijinar (DT) and Xi Taijinar (XT) Salt Lakes have been extensively researched for their mineral richness. However, the composition and distribution of their microbial communities are still poorly known. In this study, we employed metagenomic sequencing to explore the diversity and potential functions of the microbial populations in DT and XT. Our findings indicate that the salinity levels in DT (332.18–358.30 g/L) were tenfold higher than in XT (20.09–36.83 g/L). Notably, archaea dominated the DT domain at 96.16%, while bacteria prevailed in XT at 93.09%. In DT, the bacterial community comprised 33 phyla and 1717 genera, with Marinobacter emerging as the dominant genus, showing a positive correlation with the total phosphorus content. The archaeal community in DT included four main phyla and 153 genera. The most abundant genera were Natronomonas (24.61%) and Halorubrum (23.69%), which had a strong positive correlation with the concentrations of Na+, Ca2+, and Cl−. Conversely, XT hosted 33 phyla and 1906 bacterial genera, with Loktanella as the dominant genus. The archaeal taxonomy in XT encompassed four phyla and 149 genera. In both salt lakes, Proteobacteria and Euryarchaeota were the most abundant bacterial and archaeal phyla, respectively. Our analysis of the halophilic mechanisms of these microorganisms suggests that the bacteria in XT tend to synthesize compatible solutes, whereas the archaea in DT adopt a 'salt-in' strategy, integrating salt into their cellular machinery to cope with the high-salinity environment. [ABSTRACT FROM AUTHOR]