Tectonic activity shapes geothermal systems, yet its influence on microbial biogeography remains poorly resolved. This study investigates how distinct tectonic settings—comparing hot springs along the convergent margin of Yunnan-Tibet and the divergent margin of the Baikal Rift—govern their hydrochemical properties and, consequently, their microbial communities. The results reveal pronounced differences: Yunnan-Tibet springs, influenced by deep crustal processes, exhibit high ion concentrations (e.g., Na⁺, K⁺, and Cl⁻) and are dominated by thermophilic taxa like
Acetothermia,
Anaerolineae,
Bacteroidia,
Chloroflexia, and
Deinococci, which correlate positively with temperature and ion concentrations. In contrast, Baikal Rift hot springs, associated with shallower rift-related processes, are primarily characterized by
Gammaproteobacteria and
Cyanobacteria, showing a negative correlation with temperature and ion levels but a positive association with higher pH. Multivariate analyses confirm that tectonic setting is a key factor driving hydrochemical diversity, which in turn shapes microbial community structure. Despite local geochemical variations, microbial assemblages consistently cluster by their tectonic origin, highlighting the fundamental influence of plate dynamics on the assembly of geothermal ecosystems. These findings provide clear evidence that deep-seated tectonic processes significantly influence the composition and diversity of microbial life in extreme environments.