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The purpose of our investigations was to identify the photosynthetic functional peculiarities of apple variety Florina using the fluorometric method and depending on the leave position on the shoot, presence/absence of the photo-assimilating acceptor (fruit) and their correlation with the morphoanatomic support. These investigations aimed at the improvement of tree canopy architecture with the identification of the zone with maximum photosynthetic efficiency of leaves during photoinhibitory stress. The functional characteristics of photosynthetic apparatus: Effective Quantum Photosynthetic Yield of PSII, Electron Transport Rate, Instantaneous fluorescence, Maximal fluorescence, Photochemical quenching, non-photochemal quenching have been related to morpho-anatomic characteristics of leaves: cells, cell volume, internal surface of the lamina, lamina thickness, palisade tissue height, spongy tissue height, mezophillic coefficient, specific density of the cells. The results show, that during vegetation season of 2012, plants suffered from photoinhibitory stress expressed into functional characteristics of photosynthetic apparatus: high values of non-photochemical quenching, low value of electron transport rate. Structural-functional comparative analysis has shown, that leaves with top position have an effective photoprotective mechanism against high light intensity and efficiently use both effective quantum photosynthetic yield of PSII and electron transport rate.