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Thallium (Tl) is a trace element with extreme toxicity. Widespread Tl pollution in riverine systems, mainly due to escalating mining and smelting activities of Tl-bearing sulfide minerals, has attracted increasing attention. Insights into the function of the microbial communities with advanced characterization tools are critical for understanding the biogeochemical cycle of Tl. Herein, microbial communities and their adaptive evolution strategies in river sediments from a representative Tl-bearing pyrite mine area in southern China were profiled via 16S rRNA gene sequence analysis and shotgun metagenomic analysis. In total, 64 phyla and 778 genera of microorganisms were observed in the studied sediments. The results showed that pH, Tl, Pb, Zn and total organic carbon (TOC) had a significant influence on microbial community structure. Some important reductive microorganisms (such as Erysipelothrix , Geobacter , desulfatiferula , desulfatihabadium and fusibacter) were involved in the biogeochemical cycle of Tl. The ruv , rec , ars and other resistance genes enhanced the tolerance of microorganisms to Tl. The study suggested that relevant C, N and S cycle genes were the main metabolic paths of microorganisms surviving in the high Tl-polluted environment. The findings were critical for establishment, operation and regulation in the microbial treatment of Tl containing or related wastewater. Unlabelled Image • The metabolism of microbes in high thallium (Tl) polluted sediments was insighted. • Metabolite of iron/sulfate-reducing microbes might change Tl geochemical fractions. • Resistance genes such as ruv , rec and ars may enhance the microbes' tolerance to Tl. [ABSTRACT FROM AUTHOR]