The ecological characterization of the mangroves of Ngazidja was carried out in order to provide a complete study concerning especially, the ecology of mangroves, their state of conservation, their mode of use, and their capacity to sequester carbon. The study of these mangroves was carried out from biological inventories and ethnobotanical surveys. Indeed, seven species of mangroves distributed in six families were described in this work. The study of natural regeneration, shows an average rate of regeneration in some sites and a low rate in others. The global warming, exposes the coastal areas to natural disasters. Faced with these problems, this work strives to find effective solutions to mitigate these phenomena. This study focused on the estimation of carbon stored by the mangroves of Ngazidja. The results showed that carbon sequestration is proportional to the density and maturity of trees. Therefore, a good management of mangroves and reforestation of mangroves can increase within a few years the amount of carbon sequestered and consequently, reduce GHG.