<p>Tectonic activity shapes geothermal systems, yet its influence on microbial biogeography remains poorly resolved. Here, we investigate how tectonic activity influences geothermal systems and their microbial communities by comparing hot springs situated along convergent (Yunnan-Tibet) and divergent (Baikal Rift) margins. The results show that hydrochemistry and microbial community in these two tectonically different regions exhibit pronounced differences: Yunnan-Tibet hot springs, shaped by deep crustal interactions, show high concentrations of Na⁺, K⁺, and Cl⁻ ions and are dominated by thermophilic microbes such as <i>Acetothermia, Anaerolineae, Bacteroidia, Chloroflexia</i>, and <i>Deinococci</i>. These microbial groups exhibit correlations with environmental factors like temperature and ion concentrations. Conversely, Baikal Rift hot springs, associated with shallower rift-related processes, are primarily inhabited by <i>Gammaproteobacteria</i> and <i>Cyanobacteria</i>, which are negatively correlated with temperature and ion levels but positively associated with higher pH. Multivariate statistical analyses confirm that the tectonic setting is an important factor driving hydrochemical diversity, which in turn shapes microbial community structure. Despite localized geochemical variability, microbial assemblages tend to cluster strongly according to their tectonic origin, highlighting the fundamental influence of plate dynamics on the assembly of geothermal microbial ecosystems. These results provide evidence that tectonic processes exert a significant influence on the composition and diversity of microbial communities in extreme environments.</p>