Mangroves are highly productive coastal ecosystem that have high potential to capture and store atmospheric carbon in their living biomass and sediments; so called ‘blue carbon’; playing a remarkable role in coastal carbon cycle and which makes them an effective tool in global climate change mitigation. However, the intrinsic relationship of ecological elements to mangrove carbon sequestration is vital in promoting mangrove restoration and conservation. In the present study, we quantified the blue carbon capacity of eight natural mangrove stands on the Sri Lankan coast and investigated the ecological influence on their community structure and carbon sequestration potential. We employed a combination of allometry for floral carbon and sediment core extraction for sediment carbon assessment. We studied forest structure with a 10 m wide belt transect at six points in each site (n=48) and to measure edaphic influence we took three water samples by the adjoining lagoon/estuary. In order to measure sediment carbon, we extracted sediment cores at the points of the survey up to a depth of 45 cm and then were subsampled to 15 cm each. Floristic carbon was calculated with allometry while sediment organic carbon was measured and analyzed with the use of an elemental analyzer. We identified 20 true-mangrove species distributes heterogeneously with the community’s structure dominated by Avicennia marina, Avicennia officinalis, Brugueira cylindrica, Excoecaria indica, Rhizophora mucronata, and Sonneratia alba. Whole ecosystem carbon stocks were significantly different between the sites and different climatic zones (p<0.05) with the highest carbon content in Rekawa (1247.28 MgC ha-1) and the lowest in Mannar (307.82 MgC ha-1). Mean carbon content was the highest in the intermediate zone (180.36 ± 46.20 MgC ha-1). On average, the sediment carbon stock was 89% of the total carbon while higher proportion of the rest was aboveground biomass. Distance based redundancy analysis (dbRDA) showed that salinity and dissolved oxygen together with precipitation influenced species distribution across the sites. Correlation analysis revealed that the ecosystem carbon stocks are highly influenced by forests structural variables including tree density and taxonomic diversity, and ecological variables such as dissolved oxygen, salinity and precipitation. From the analysis, we found out that if the said mangroves are disturbed by any means of land-use changes, they could emit an equivalent (mean ± SD) 2584.13 ± 1061.23 Mg ha-1 of carbon dioxide. This could possibly play a critical role in the climate change mitigation agenda. In summary, the Sri Lankan mangroves holds a substantial asset for national and global blue carbon management and therefore climate change mitigation policy. In addition, the potential carbon sequestration and other co-benefits that these mangrove ecosystems provide would be lost if high intensity land-use change were to occur across these estates. The key findings from this thesis will be an essential to guide policymakers and will inform climate change mitigation strategies at both regional and national scales.