This study estimated the total ecosystem carbon stock (TECS) and sediment carbon sequestration rate through burial for fragmented mangrove habitats of Kochi, south-west coast of India. The mean TECS of Kochi mangroves was estimated at 335.33 ± 184.47 t C ha⁻¹, with above ground biomass of 171.68 ± 104.42 t C ha⁻¹, belowground biomass of 83.30 ± 41.98 t C ha⁻¹, litterfall carbon as dead biomass of 7.12 ± 2.81 t C ha⁻¹ and soil carbon stock of 73.22 ± 39.40 t C ha⁻¹. The average historical soil carbon sequestration rate of Kochi mangroves was also estimated as 2.95 t C ha⁻¹ yr⁻¹. The study revealed that there was significant variability in TECS and sediment carbon burial rate among riverine, estuarine and marine mangrove habitats and it appears that, the biological factors especially mangrove plant structure, species, age, litterfall production, crab density, mangrove conversion to aquaculture ponds and other urban pressure played major roles in driving the variability in carbon stocks and storage. While the sediment particle size, bulk density and the environmental settings played a secondary role. Very low TECS and soil carbon sequestration rate was found in aquaculture converted mangrove habitat. The CO_2e of ecosystem carbon stock (496311.20 t CO₂ e) and soil CO₂ burial (10.62 t CO₂ e ha⁻¹ yr⁻¹ respectively) of mangroves of Kochi, revealed that even with high urban pressure and anthropogenic activities which resulted in fragmented distribution, they are still potent in long term carbon sequestration unless it is not further disturbed. Therefore, conservation and restoration of mangrove habitats based on understanding of the regional controlling factors of carbon stock and carbon burial is a need for scientific climate change mitigation efforts. The study will also contribute to fill the gaps in global mangrove carbon stock assessments for avoiding uncertainties.