Mangrove forests occupy less than 1% of tropical forest areas, but they represent approximately 3% of worldwide tropical forest carbon capture. The present study quantified carbon stocks in mangrove forests in two bays in the Colombian Pacific, and evaluated the effect of forest structure on variations of carbon storage in the different ecosystem compartments. Significant differences were found in carbon stocks between the stations of Málaga Bay (a national marine park) and Buenaventura Bay (the main harbor area). Belowground biomass and sediment represented the greatest carbon stocks in the forest. Carbon reserves in mangroves in the Colombian Pacific were similar compared with other tropical mangrove areas. These results highlight the importance of evaluating carbon storage in these ecosystems and of formulating conservation and management strategies integrated with the mangrove forest in the Colombian Pacific