<p>Tropical wetlands are the largest natural source of methane on Earth, yet they remain the least studied, particularly high-altitude wetlands like those in the Páramo of Chingaza, Colombia. These ecosystems are crucial for water provisioning, carbon sequestration, and biodiversity conservation but are threatened by rapid climate change. While the páramo biome supports thousands of endemic plant species and plays a vital role in balancing carbon inputs and greenhouse gas outputs (CO₂ and CH₄), its soil microbial diversity and functional roles in soil processes are largely unexplored. To fill this knowledge gap, we conducted amplicon sequencing of the ITS, 16S rRNA, and 18S rRNA genes to examine microbial diversity across three distinct ecosites at Laguna Seca, Chingaza, characterized by different macrotopographies, water-table levels, and vegetation assemblages. Our findings revealed significant variations in microbial community structure, with the peatland ecosite showing the highest diversity across all amplicons. Comparative analysis with global wetland datasets indicated that microbial communities at Laguna Seca share similarities with subarctic Stordalen Mire fen and other peat-forming wetlands. Notably, our targeted assessment identified a diversity of potential methanogens and methanotrophs exclusively within the peatland ecosite, at low but comparable abundance to other wetlands. This suggests that methane cycling in the other ecosites of this wetland may either be less prominent than expected or involve organisms not previously associated with known methane processes. These findings establish a baseline for understanding microbial diversity in tropical high-montane wetlands and underscore the unique ecological significance of páramo peatlands amid climate change.</p>