Mangrove forests, crucial carbon-rich ecosystems, are increasingly vulnerable to soil carbon loss and greenhouse gas (GHG) emissions due to human disturbance. However, the contribution of mangrove trees to GHG emissions remains poorly understood. This study monitored CO₂, CH₄, and N₂O fluxes from the stems of two mangrove species, native Kandelia obovata (KO) and exotic Sonneratia apetala (SA), at three heights (0.7 m, 1.2 m, and 1.7 m) during the dry winter period on Qi'ao Island, Pearl River Estuary, China. Heartwood samples were analyzed to identify potential functional groups related to gas fluxes. Our study found that tree stems acted as both sinks and sources for N₂O (ranging from −9.49 to 28.35 μg m⁻² h⁻¹ for KO and from −6.73 to 28.95 μg m⁻² h⁻¹ for SA) and CH₄. SA exhibited significantly higher stem CH₄ flux (from −26.67 to 97.33 μg m⁻² h⁻¹) compared to KO (from −44.13 to 88.0 μg m⁻² h⁻¹) (P < 0.05). When upscaled to the community level, both species were net emitters of CH₄, contributing approximately 4.68 % (KO) and 0.51 % (SA) to total CH₄ emissions. The decrease in stem CH₄ flux with increasing height, indicates a soil source. Microbial analysis in the heartwood using the KEGG database indicated aceticlastic methanogenesis as the dominant CH₄ pathway. The presence of methanogens, methanotrophs, denitrifiers, and nitrifiers suggests microbial involvement in CH₄ and N₂O production and consumption. Remarkably, the dominance of Cyanobacteria in the heartwood microbiome (with the relative abundance of 97.5 ± 0.6 % for KO and 99.1 ± 0.2 % for SA) implies roles in carbon and nitrogen fixation for mangroves coping with nitrogen limitation in coastal wetlands, and possibly in CH₄ production. Although the present study has limitations in sampling duration and area, it highlights the significant role of tree stems in GHG emissions which is crucial for a holistic evaluation of the global carbon sequestration capability of mangrove ecosystems. Future research should broaden spatial and temporal scales to enhance the accuracy of upscaling tree stem gas fluxes to the mangrove ecosystem level.