The effect of rootstock on scion photosynthesis can be quite marked. Reduced hydraulic conductivity at the graft union can negatively affect stomatal conductance, which in turn may diminish gas exchange and photosynthesis. Under high light intensities this condition can worsen, as a proportionally smaller fraction of intercepted photons can be utilized in the photosynthetic process. The excess photons are dissipated either via photoprotective mechanisms (Non-Photochemical-Quenching; Alternative Transports; Photorespiration) or photooxidation, with the production of Active Oxygen Species (AOS). Under reduced photosynthetic activity, the defense mechanisms and photooxidation reactions increase, to cope with excess energy which cannot be utilized for carboxylation. This paper reports a study, conducted on leaves of the pear 'Bosc' grafted on seedling and quince EMC rootstocks, detailing their behavior under conditions of similar light and temperature. Stomatal conductance and transpiration were consistently higher in the trees on seedling than on EMC, which resulted in greater photosynthetic activity in the leaves of the former. Because of the stomatal limitation, trees oil EMC allocated less energy to the photosynthetic process, as a greater proportion of intercepted photons was either dissipated via the Non-Photochemical Quenching (NPQ) cycle or damaged Photosystem II (PSII). Somewhat surprisingly, Alternative Transports (Water-Water Cycle; Cyclic Transport around PSI; Glutathione-Ascorbate Cycle) and Photorespiration in quince were consistently lower than in seedling-grafted trees in the early morning. In conclusion, rootstocks can affect the photosynthetic potential of the grafted tree, in relation to their graft compatibility, although more work is needed to understand the degree of reduction due to photo-oxidative stress.