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The magnesium atom of chlorophylls (Chls) is always five- or six-coordinated within chlorophyll-protein complexes which are the main light-harvesting systems of plants, algae and most photosynthetic bacteria. Due to the presence of stereocenters and the axial ligation of magnesium the two faces of Chls are diastereotopic. It has been previously recognized that the alpha-configuration having the magnesium ligand on the opposite face of the 17-propionic acid moiety is more frequently encountered and is more stable than the more seldom beta-configuration that has the magnesium ligand on the same face [T.S. Balaban, P. Fromme, A.R. Holzwarth, N. Kraubeta, V.I. Prokhorenko, Relevance of the diastereotopic ligation of magnesium atoms in chlorophylls in Photosystem I, Biochim. Biophys. Acta (Bioenergetics), 1556 (2002) 197-207; T. Oba, H. Tamiaki, Which side of the pi-macrocycle plane of (bacterio)chlorophylls is favored for binding of the fifth ligand? Photosynth. Res. 74 (2002) 1-10]. In photosystem I only 14 Chls out of a total of 96 are in a beta-configuration and these occupy preferential positions around the reaction center. We have now analyzed the alpha/beta dichotomy in the homodimeric photosystem II based on the 2.9 A resolution crystal structure [A. Guskov, J. Kern, A. Gabdulkhakov, M. Broser, A. Zouni, W. Saenger, Cyanobacterial photosystem II at 2.9 A resolution: role of quinones, lipids, channels and chloride, Nature Struct. Mol. Biol. 16 (2009) 334-342] and find that out of 35 Chls in each monomer only 9 are definitively in the beta-configuration, while 4 are uncertain. Ab initio calculations using the approximate coupled-cluster singles-and-doubles model CC2 [O. Christiansen, H. Koch, P. Jørgensen, The second-order approximate coupled cluster singles and doubles model CC2, Chem. Phys. Lett. 243 (1995) 409-418] now correctly predict the absorption spectra of Chls a and b and conclusively show for histidine, which is the most frequent axial ligand of magnesium in chlorophyll-protein complexes, that only slight differences (<4 nm) are encountered between the alpha- and beta-configurations. Significant red shifts (up to 50 nm) can, however, be encountered in excitonically coupled beta-beta-Chl dimers. Surprisingly, in both photosystems I and II very similar "special" beta-beta dimers are encountered at practically the same distances from P700 and P680, respectively. In purple bacteria LH2, the B850 ring is composed exclusively of such tightly coupled beta-bacteriochlorophylls a. A statistical analysis of the close contacts with the protein matrix (<5 A) shows significant differences between the alpha- and beta-configurations and the subunit providing the axial magnesium ligand. The present study allows us to conclude that the excitation energy transfer in light-harvesting systems, from a peripheral antenna towards the reaction center, may follow preferential pathways due to structural reasons involving beta-ligated Chls.