Oxygen and CO2 fluxes were measured in situ as a function of depth on colonies of two species of the zooxanthellate coral Stylophora and were used to compute metabolic quotients. We report for the first time on the photosynthetic quotient of zooxanthellae in hospite (PQz); it ranges from 1.14 to 1.57 and depends on the light regime (daily photosynthetic photon flux density). The comparative effect of light on PQz and on the respiratory quotient of the coral suggests that glycerol is the main substance photosynthesized, translocated, and consumed in shallow‐water colonies, whereas it is replaced by lipid with decreasing light (increasing depth). Such a result is potentially important for the energy budget considerations of any plant‐animal endosymbiosis and provides some evidence that light controls the quality of products photosynthesized by the plant and catabolized by the host.