The mechanisms underlying stabilization of soil organic matter (SOM) in coastal ecosystems, including mangrove forests, are poorly understood, limiting our ability to predict the consequences of disturbances. Here, we introduce density fractionation to mangrove soils to identify the distribution and properties of the functional components of SOM with regard to degradation state, stability, and origin, namely, the high-density fraction (HF), free low-density fraction (f-LF), and mineral-associated LF (m-LF). Three soil cores (1 m) were collected in a mangrove forest on Ishigaki Island, Japan and cut into 10 cm intervals and analyzed. The massive production of mangrove fine roots resulted in a high abundance of LFs throughout the cores, which markedly differed from terrestrial soils. Relative abundance of LFs together accounted for 38%–66% of total soil C. The m-LF was as abundant as f-LF and 1.6 times higher in relative abundance than the global average of terrestrial soils. The C/N ratios and δ13C values clearly increased with depth in all fractions, which was attributed to the increased contribution from roots. We found a consistent pattern in Δ14C values of density fractions. HF was the oldest with Δ14C between -149‰ and -97‰ followed by m-LF (between -130‰ and -87‰) and then f-LF (between -89‰ and 78‰), suggesting that mineral association may be pivotal in long-term carbon storage in the mangrove mineral soil. Our analysis successfully identified meaningful functional components of mangrove SOM, yet several questions remained unanswered, including a large variability in Δ14C in different cores. Future studies would benefit from a coupled analysis of quantity and quality of density fractions and geochemical factors in the mangrove soil.