Thallium (TI) is a highly toxic metalloid and is considered a priority pollutant by the US Environmental Protection Agency (EPA). Currently, few studies have investigated the distribution patterns of bacterial and fungal microbiomes in TI-impacted environments. In this study, we used high-throughput sequencing to assess the bacterial and fungal profiles along a gradient of TI contents in TI mine waste rocks in southwestern China. Our results showed that TI had an important, but different influence on the bacterial and fungal diversity indices. Using linear regression analysis, we furtherly divided the dominant bacterial and fungal groups into three distinct microbial sub-communities thriving at high, moderate, and low levels of TI. Furthermore, our results also showed that TI is also an important environmental variable that regulates the distribution patterns of ecological clusters and indicator genera. Interestingly, the microbial groups enriched in the samples with high TI levels were mainly involved in metal and nutrient cycling. Taken together, our results have provided useful information about the responses of bacterial and fungal groups to TI contamination. (C) 2020 Elsevier Ltd. All rights reserved.