Geothermal ecosystems are underexplored reservoirs of microbial diversity with significant biogeochemical and biotechnological implications. This study presents a high-resolution metagenomic analysis of thermophilic microbial communities in the hot mud of Linow Lake, a tropical geothermal system in Indonesia’s Wallacea Zone a region straddling the Pacific and Mediterranean volcanic cirques. Using 16S rRNA gene sequencing and co-occurrence network analysis, we identified a microbial community dominated by Proteobacteria (65% Burkholderiaceae, 24.6% Corynebacteriaceae), with novel, unclassified taxa (0.1%), highlighting the site’s unique biodiversity. Network analysis revealed tightly clustered functional guilds, suggesting metabolic syntrophy in sulfur cycling and organic matter degradation under extreme temperature (50-98 °C) and acidic (pH 2-4) conditions. Notably, the dominance of Burkholderia and Corynebacterium genera implies adaptive strategies for heavy metal resistance and bioactive compound synthesis. These findings underscore the ecosystem’s role in global biogeochemical cycles and its untapped potential for industrial applications, including thermostable enzyme production and bioremediation. Our work bridges critical gaps in understanding tropical geothermal microbiomes and positions Linow Lake as a key site for exploring microbial evolution and bioprospecting in multi-stress environments.