| Summary: | Mangroves are one of the blue carbon ecosystems. However, greenhouse gas emissions from mangrove soils may reduce the capacity of carbon storage in these systems. In this study, methane (CH<sub>4</sub>) fluxes and soil properties of the top 10 cm layer were determined in subtropical (<i>Kandelia obovata</i>) and tropical (<i>Avicennia marina</i>) mangrove ecosystems of Taiwan for a complete seasonal cycle. Our results demonstrate that CH<sub>4</sub> emissions in mangroves cannot be neglected when constructing the carbon budgets and estimating the carbon storage capacity. CH<sub>4</sub> fluxes were significantly higher in summer than in winter in the <i>Avicennia</i> mangroves. However, no seasonal variation in CH<sub>4</sub> flux was observed in the <i>Kandelia</i> mangroves. CH<sub>4</sub> fluxes were significantly higher in the mangrove soils of <i>Avicennia</i> than in the adjoining mudflats; this trend, however, was not necessarily recapitulated at <i>Kandelia</i>. The results of multiple regression analyses show that soil water and organic matter content were the main factors regulating the CH<sub>4</sub> fluxes in the <i>Kandelia</i> mangroves. However, none of the soil parameters assessed show a significant influence on the CH<sub>4</sub> fluxes in the <i>Avicennia</i> mangroves. Since pneumatophores can transport CH<sub>4</sub> from anaerobic deep soils, this study suggests that the pneumatophores of <i>Avicennia marina</i> played a more important role than soil properties in affecting soil CH<sub>4</sub> fluxes. Our results show that different mangrove tree species and related root structures may affect greenhouse gas emissions from the soils.
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