Tropical peatlands are an important carbon store and source of greenhouse gases, but the microbial component, particularly community structure, remains poorly understood. While microbial communities vary between tropical peatland land uses, and with biogeochemical gradients, it is unclear if their structure varies at smaller spatial scales as has been established for a variety of peat properties. We assessed the abundances of PLFAs and GDGTs, two membrane spanning lipid biomarkers in bacteria and fungi, and bacteria and archaea, respectively, to characterise peat microbial communities under two dominant and contrasting plant species, Campnosperma panamensis (a broadleaved evergreen tree), and Raphia taedigera (a canopy palm), in a Panamanian tropical peatland. The plant communities supported similar microbial communities dominated by Gram negative bacteria (38.9–39.8%), with smaller but significant fungal and archaeal communities. The abundance of specific microbial groups, as well as the ratio of caldarchaeol:crenarchaeol, isoGDGT: brGDGTs and fungi:bacteria were linearly related to gravimetric moisture content, redox potential, pH and organic matter content indicating their role in regulating microbial community structure. These results suggest that tropical peatlands can exhibit significant variability in microbial community abundance even at small spatial scales, driven by both peat botanical origin and localised differences in specific peat properties. © 2020, The Author(s).