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Living trees in forests emit or consume methane (CH4) and nitrous oxide (N2O) through their stems. These stem fluxes can originate directly from the internal tissues, or co-occur from soils and stems. However, the magnitudes, origins, and biogeochemical pathways of these fluxes remain poorly understood.In our study, we aimed to investigate whether tropical forest habitats (upland versus seasonally flooded areas), tree species and composition of the microbial communities living in the sapwood influence the stem fluxes of CH4 and N2O.To address this, we measured the in situ CH4 and N2O fluxes in the stems of thirteen tropical tree species using static chambers. We investigated the microbial communities in the sapwood by sequencing the 16S rDNA of bacteria and archaea on an Illumina MiSeq platform. Measurements were taken in two contrasting habitats: well-drained, nutrient-poor soil in an upland area, and waterlogged, nutrient-rich soil in a seasonally flooded area of a tropical forest in French Guiana. Fluxes, woody tissue microbial communities, and related tree traits were measured during the wet season.Overall, we observed a significant effect of forest habitat on sapwood microbial communities, which remained relatively consistent within specific tree species. Stem fluxes per unit of stem surface area were approximately 2.5 times higher for CH4 and lower for N2O in the seasonally flooded forest, compared to the upland forest. Variability in these fluxes was observed not only between the two forest habitats, but also among and within tree species. Surprisingly, methanotrophs and methanotrophs were barely detectable, and denitrifiers and nitrifiers were also scarce in the stem tissues, despite the high CH4 and, to a lesser extent, N2O emissions measured on the stem surfaces. This suggests that, in our site, CH4 and N2O fluxes mainly result from processes occurring in the heartwood, bark, soil, or a combination of these. Further research is needed to shed light on the microbial mechanisms underlying the exchange of CH4 and N2O between the trees and the atmosphere in tropical forest ecosystems.