The carbon sequestration potential of natural and restored mangrove ecosystems was assessed in Tamil Nadu and Andhra Pradesh, India. A total of eight mangrove species were recorded in the natural vegetation and the restored mangrove site. Hydrological factors, including salinity, temperature, dissolved oxygen, and pH, were measured, along with tree density, basal area, aboveground and belowground biomass, and carbon stock. The mean tree density of mangroves in the natural stand was 4199.5 ± 1348.37 trees ha− 1, and the restored site had an average of 4523.3 ± 654.02 trees ha− 1. The basal area of mangroves is from 19.24 ± 15.73 m2 to 66.58 ± 84.57 ha− 1 across both vegetation types. The average aboveground carbon stock for natural mangroves was 260.4 ± 114.15 Mg C ha− 1, whereas for the restored site, the average aboveground carbon stock was 49.21 ± 19.26 Mg C ha− 1. The total average vegetative carbon stock in natural vegetation was 346.3 ± 152.04 Mg C ha− 1, and in the restored area, the mean value was 69.45 ± 26.99 Mg C ha− 1. The natural vegetation exhibited a mean soil organic carbon (SOC) of 11.39 ± 8.4 Mg C ha − 1 and the restored site had an average value of 7.22 ± 5.33 Mg C ha-¹. The SOC content was significantly associated with the species dominance index (p < 0.01). A significant variation in total vegetative carbon was observed among the sampling sites, with the natural site showing Kruskal–Wallis test (Hc) = 29.4 (p < 0.001) and the restored site showing Hc = 18.51 (p < 0.001).