Background: Increased recognition of mangrove high carbon storage potential has prompted carbon sequestration as one of the main goals in mangrove afforestation. In southern China, the introduced fast-growing Sonneratia apetala and native Kandelia obovata have been widely afforested since the mid-1980s. While S. apetala has spread extensively, the implications and ecosystem services are yet to be ascertained. Methods: Soil/root coring was conducted in two 12-year-old S. apetala and K. obovata plantations, respectively. Fine-root mass and soil physicochemical properties were obtained and compared. Results: Fine-root mass and soil organic carbon stock ranged between 129 and 394 g m−2 and 7.9 and 15.8 Mg C ha−1, respectively. Soil organic carbon stock and fine-root mass were both significantly different between the forests. Organic carbon in soil is significantly correlated to fine-root mass and organic carbon in fine roots. Conclusions: The contribution to soil organic carbon by fine-root mass may be different between the two species. Growth and physiological traits not only may influence stand characteristics but also soil properties that drive overall carbon accumulation. Contrary to the original expectation driving the introduction, the shrubby native K. obovata may have higher potential as a carbon sink than the introduced S. apetala.