Seagrass meadows deliver a range of ecosystem services, where one of the more important is the capacity to store carbon and serve as sinks for atmospheric carbon dioxide. The capacity of seagrass meadows for carbon storage might, however, be modified and complicated by several factors; one important factor is the possible effects of calcification within the meadows. In tropical areas, seagrass meadows can contain high proportions of calcareous organisms, which through their calcification may cause release of CO2. To study this aspect of the CO2 balance within tropical seagrass systems, we investigated the air-water CO2 flux in seagrass mesocosms with different plant community compositions, i.e. mixtures of seagrass and calcifying macroalgae, having similar overall photosynthetic oxygen evolution rates. The measured CO2 fluxes changed both in rate and direction over the day and were significantly related to plant community composition. Downward fluxes of CO2 were found only over vegetation with high proportion of seagrass and in the afternoon, whereas occurrence of calcifying algae appeared to reverse the flow. A partial least squares (PLS) regression model indicated that pH, pCO2 and dissolved inorganic carbon (DIC) were the primary environmental variables predicting the CO2 fluxes. Our findings show that algal calcification might partly counteract the carbon sequestration in seagrass meadows.