Estimates of organic carbon (C org) storage by seagrass meadows which consider interhabitat variability are essential to understand their potential to sequester carbon dioxide (CO 2) and derive robust global and regional estimates of blue carbon storage. In this study, we provide baseline estimates of seagrass extent, and soil C org stocks and accumulation rates from different seagrass habitats at Rottnest Island (in Amphibolis spp., Posidonia spp., Halophila ovalis, and mixed Posidonia/Amphibolis spp. meadows). The C org stocks in 0.5 m thick seagrass soil deposits, derived from 24 cores, were 5.1 ± 0.7 kg C org m −2 (mean ± SE, ranging from 0.05 to 12.9 kg C org m −2), accumulating at 23.2 ± 3.2 g C org m −2 year −1 (ranging from 0.22 to 58.9 g C org m −2 year −1) over the last decades. There were significant differences in C org content (%) and stocks (mg C org cm −3), stable carbon isotope composition of the soil organic matter (δ 13 C), and soil grain size among the seagrass meadows studied, highlighting that biotic and abiotic factors influence seagrass soil C org storage. Mixed meadows of Posidonia/Amphibolis spp. and monospecific meadows of Posidonia spp. and Amphibolis spp. had the highest C org stocks (ranging from 6.2 to 6.4 kg C org m −2), while Halophila spp. meadows had the lowest C org stocks (1.2 ± 0.6 kg C org m −2). We estimated a total soil C org stock of 48.1 ± 8.5 Gg C org beneath the 755 ha of Rottnest Island's seagrasses, and a C org sequestration capacity of 0.81 ± 0.06 Gg C org year −1 , which is equivalent to the sequestration of ∼22% of the island's current annual CO 2 emissions. Our results contribute to the existing global dataset on seagrass soil C org storage and show a significant potential of seagrass to sequester CO 2 , which are particularly relevant in the context of achieving carbon neutrality through conservation actions in environmentally-marketed, tourist destinations such as Rottnest Island.