Mangroves are recognized as one of the richest carbon storage systems. However, the factors regulating carbon sinks in mangrove ecosystems are still unclear, particularly in the subtropical mangroves. The biomass, production, litterfall, detrital export and decomposition of the dominant mangrove vegetation in subtropical (Kandelia obovata) and tropical (Avicennia marina) Taiwan were quantified from October 2011 to July 2014 to construct the carbon budgets. Despite the different tree species, a principal component analysis revealed the site or environmental conditions had a greater influence than the tree species on the carbon processes. For both species, the net production (NP) rates ranged from 10.86 to 27.64MgCha-1 year-1 and were higher than the global average rate due to the high tree density. While most of the litterfall remained on the ground, a high percentage (72%-91%) of the ground litter decomposed within 1year and fluxed out of the mangroves. However, human activities might cause a carbon flux into the mangroves and a lower NP rate. The rates of the organic carbon export and soil heterotrophic respiration were greater than the global mean values and those at other locations. Only a small percentage (3%-12%) of the NP was stored in the sediment. The carbon burial rates were much lower than the global average rate due to their faster decomposition, indicating that decomposition played a critical role in determining the burial rate in the sediment. The summation of the organic and inorganic carbon fluxes and soil heterotrophic respiration well exceeded the amount of litter decomposition, indicating an additional source of organic carbon that was unaccounted for by decomposition in the sediment. Sediment-stable isotope analyses further suggest that the trapping of organic matter from upstream rivers or adjacent waters contributed more to the mangrove carbon sinks than the actual production of the mangrove trees.