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Aims: Mangrove ecosystems can help mitigate climate change by sequestering significant amounts of carbon (C) from the atmosphere and ocean, contributing to regional "blue carbon" stocks. However, it is unclear whether non-native species introduced in coastal wetlands can function as a more efficient carbon sink. Methods: By examining two dominant mangrove species, native Kandelia obovata (KO) and exotic Sonneratia apetala Buch.-Ham. (SA), at the Qi'ao Island, China, we quantified and compared ecosystem C storage, C sequestration rate, source and stability of soil organic carbon (SOC) under different vegetation covers. Results & conclusion: Our results showed that both species acted as strong carbon sinks relative to mudflat reference, with overall ecosystem C storage being comparable under KO (410 Mg C ha−1) and SA with different stand ages (224–452 Mg C ha−1), but a few times higher than corresponding unvegetated mudflat. However, by excluding SOC accumulation from prior land use (i.e., unvegetated mudflat), non-native species (i.e., SA) showed a significantly higher ecosystem carbon sequestration rate (8.2–16.4 Mg C ha−1 yr−1) than native KO (4.5 Mg C ha−1 yr−1), owing largely to fast biomass carbon sequestration in SA ecosystem. Relative to mudflat reference, the input of autochthonous source (mangrove tissues) contributed substantially to additional carbon sequestration under mangroves. It should be noted that the relative size of carbon sequestration in non-native mangroves is also affected by factors related to ecosystem, climate, soil properties and land use, the differences still exist among locations, and ecosystem modeling with field validation is desirable for regional estimation of carbon stocks and sequestration rates. [ABSTRACT FROM AUTHOR]