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Mangroves play an important role in carbon sequestration. However, mangroves can be sources of greenhouse gas (GHG) emissions. In this study, methane (CH₄) emissions and related soil properties were determined in multiple mangroves in Taiwan, including <i>Kandelia obovata</i> and <i>Avicennia marina</i> mangroves. <i>K. obovata</i> possess prop roots, whereas pneumatophores are found in <i>A. marina</i>. Our results showed that mangrove soils were significant sources of CH₄ emissions, which should be accounted for in mangrove carbon budgets. In particular, CH₄ emissions in the <i>A. marina</i> mangroves were approximately 50- to 100-fold those of the <i>K. obovata</i> mangroves and the adjoining mudflats. Multiple regression analyses indicated that the soil salinity and pH in <i>K. obovata</i> mangroves and the soil redox potential and organic content in the mudflats were the key factors affecting CH₄ emissions. However, the pneumatophore density alone explained approximately 48% of the variation in CH₄ emissions in the <i>A. marina</i> mangroves. More pneumatophores resulted in higher CH₄ emissions in the <i>A. marina</i> mangroves. Thus, compared with the assessed soil properties, the contribution of pneumatophores to the transportation of CH₄ from soil was more significant. In addition to soil properties, our results demonstrated that the root structure may also affect GHG emissions from mangroves.