Seagrass beds are important carbon sinks that play a potential role in climate mitigation. The amount of carbon stored in seagrass ecosystems is greatly determined by the size of the seagrass species. This study aimed to determine the differences between carbon stocks in large seagrass represented by Thalassia hemprichii and smaller seagrass represented by Cymodocea rotundata in Pramuka Island, Seribu Islands, DKI Jakarta (Daerah Khusus Ibukota Jakarta). Four stations were selected purposively to represent sites with different densities and predominant species. The parameters measured were characteristics of seagrass (species density, leaf area, biomass, and carbon stock) and environmental parameters (water depth and sediment grain size distribution). Seagrass carbon stock was measured using the Loss on Ignition (LOI) method. The results showed that the seagrass T. hemprichii had a higher density, leaf area, biomass, and carbon stock than those C. rotundata. The carbon stock of T. hemprichii in Pramuka Island was 18.22–443.73 g C m-2 while C. rotundata was 5.99–25.61 g C m-2. Moreover, large seagrasses have great potential to deposit more carbon in seagrass sediments. The analysis using PCA showed a relationship between the size of seagrass morphology and the amount of carbon stock. This study shows that seagrasses with large morphology strongly support the high value of carbon stocks stored in seagrass ecosystems.