Seagrass ecosystem is one of the coastal ecosystems that can absorb carbon and subsequently store it at a high capacity. This research aimed to study carbon stocks in biomass based on seagrass type and density, differences in carbon stocks between below-ground and above-ground, and the potential for carbon storage of the seagrass ecosystem on the coast of Waai and Liang, Ambon Island. Five seagrass species species were found, including Enhalus acoroides, Halophila ovalis, Halodule pinifolia, Thalassia hemprichii and Cymodocea rotundata,. Based on the results, halassia hemprichii was predominant in Liang waters and Halodule pinifolia was predominant in Waai waters. The highest seagrass biomass in both the below ground and above ground was found for Cymodocea rotundata in Waai waters and Thalassia hemprichii in Liang waters. The total carbon stock in Liang waters was 39.75 gC/m2, whereas that in Waai waters was 56.46 gC/m2. The results showed that the total carbon stock below ground was much greater than above ground, suggesting that more carbon is stored below seagrass substrate than above it in both Waai and Liang coastal waters.