Seagrass ecosystems are important contributors to mitigation of climate change, since they are responsible for large carbon sinks. However, there is limited knowledge regarding the importance of variability of carbon storage in various ecosystems. In this study, we estimated carbon storage in several structurally different seagrass meadows along the west coast of Thailand and determined whether degree of exposure, human disturbance, and meadow type influenced carbon storage within these meadows. Carbon content within the living vegetation was on average 3±2.7 Mg ha −1 , whilst average storage of carbon in the sediment was 122±35.3 Mg ha −1 . Meadow type and disturbance had a significant influence on total carbon storage in the ecosystem, while the degree of exposure of the bay did not show great differences. Uniform meadows had a higher average total carbon storage than mixed meadows (133±36.2 and 110±41.3 Mg ha −1 , respectively). Undisturbed meadows had a higher average total carbon storage than disturbed ones (140±36.5 and 103±34.8 Mg ha −1 , respectively). The results obtained contribute to our understanding of carbon storage on an ecosystem scale and can provide a baseline for proper management, conservation, and climate change studies in the region.