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 Kandelia obovata and Avicennia marina mangroves. K. obovata possess prop roots, whereas pneumatophores are found in A. marina. 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 A. marina mangroves were approximately 50- to 100-fold those of the K. obovata mangroves and the adjoining mudflats. Multiple regression analyses indicated that the soil salinity and pH in K. obovata 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 A. marina mangroves. More pneumatophores resulted in higher CH4 emissions in the A. marina 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.