Blue carbon assessments are typically based on contemporary measurements of carbon stocks and burial rates, providing limited insight into the long-term ecological processes that regulate carbon sequestration. Fossil pollen records have been widely used to reconstruct past vegetation dynamics, but their potential to inform long-term blue carbon dynamics remains largely unexplored. Here, we investigate whether fossil pollen archives can provide a historical perspective on blue carbon ecosystem development by linking changes in mangrove vegetation with long-term carbon accumulation patterns. To address this question, we compare multiproxy sediment records from two contrasting mangrove ecosystems: the Zhangjiang Estuary in subtropical China and the Pichavaram mangroves in tropical India. Both records integrate fossil pollen analysis with sediment geochemistry and robust chronological reconstruction, enabling vegetation history to be evaluated alongside indicators of ecosystem condition and carbon storage. In Zhangjiang, a two-century record reveals repeated disturbance–recovery cycles associated with hydrological modification, land reclamation, aquaculture expansion, and subsequent conservation efforts. Intervals characterized by high mangrove pollen abundance (>40%) correspond with elevated soil organic carbon stocks (>80 Mg C ha⁻¹), whereas disturbance phases are marked by reduced mangrove representation, increased herbaceous taxa, and lower carbon storage. Remote-sensing analyses further indicate an approximately fivefold increase in mangrove extent following conservation measures implemented since the 1990s. The Pichavaram record provides a complementary tropical perspective. Fossil pollen assemblages reveal a historically more diverse mangrove community, including evidence for the former occurrence of Sonneratia griffithii, a species absent from the modern ecosystem. The transition toward simplified contemporary assemblages coincides with comparatively lower soil organic carbon stocks (approximately 26–28 Mg C ha⁻¹), suggesting long-term linkages between vegetation composition and blue carbon potential. Across both systems, major shifts in pollen assemblages coincide with measurable changes in carbon-related ecosystem properties. While fossil pollen cannot directly quantify carbon stocks, it preserves information on mangrove dominance, biodiversity change, and ecosystem transitions that provide valuable context for interpreting long-term blue carbon trajectories. Our findings highlight the potential of paleoecological records to complement contemporary blue carbon assessments by extending ecological baselines beyond the timescales captured by direct measurements and improving our understanding of how biodiversity change, disturbance, and restoration influence carbon sequestration in mangrove ecosystems.