Fluxes of dissolved inorganic carbon and oxygen at the water-sediment interface were measured at eight coral reef stations (Indian Ocean) in summer and winter. The dark fluxes provided the community respiratory quotient (CRQ = dissolved inorganic carbon release / oxygen uptake) and the diurnal fluxes corrected from the dark fluxes gave the community photosynthetic quotient (CPQ = oxygen gross release / dissolved inorganic carbon gross uptake). The CRQ and the winter CPQ were not significantly different from 1. Summer CPQ (0.79; SD 0.02) was significantly lower than 1 due to the combined effect of the daily evolution of the community respiration and the discrepancy between the daily evolution in community oxygen respiration and community carbon respiration. These results highlight the importance of measuring simultaneously the benthic community production and respiration for long term integrated data sets, instead of the traditional daily or seasonal budget calculations from limited measures of community respiration.