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Non-native species are expanding globally and can alter ecosystem functions, including food web dynamics, community structure and carbon storage. Seagrass are foundation species that contribute a variety of ecosystem services in near-shore coastal ecosystems, including a significant sink of carbon. In the Caribbean, the rapidly expanding non-native Halophila stipulacea has unknown impacts on carbon storage. To investigate the impacts on carbon storage, we quantified organic carbon (C org) content in sediment and seagrass tissues from monotypic H. stipulacea beds, mixed native seagrass beds dominated by Thalassia testudinum and Syringodium filiforme, and unvegetated substrate in St. John, USVI. We found native seagrass-vegetated sediment contained 1.3 times more C org than sediment covered by H. stipulacea , and 1.6 times more C org than unvegetated areas on average. Whereas, H. stipulacea -dominated substrate stored 1.2 times more C org than unvegetated substrate. Likewise, native species contained 2.2 times more aboveground biomass and 6.0 times more belowground biomass than H. stipulacea. Since seagrasses are critical sources of carbon sequestration, our results suggest that invading H. stipulacea is associated with lower carbon stocks which has potential implications for conservation activities and climate change mitigation. [Display omitted] • Non-native species are expanding globally and can alter ecosystem functions. • Our results suggest that invading H. stipulacea is associated with lower carbon stocks. • In the Caribbean, rapidly expanding Halophila stipulacea may reduce carbon storage. [ABSTRACT FROM AUTHOR]