The monomeric chlorophyll, Chl(D1), which is located between the PD1PD2 chlorophyll pair and the pheophytin, Pheo(D1), is the longest wavelength chlorophyll in the heart of Photosystem II and is thought to be the primary electron donor. Its central Mg2+ is liganded to a water molecule that is H-bonded to D1/T179. Here, two site-directed mutants, D1/T179H and D1/T179V, were made in the thermophilic cyanobacterium, Thermosynechococcus elongatus, and characterized by a range of biophysical techniques. The Mn4CaO5 cluster in the water-splitting site is fully active in both mutants. Changes in thermoluminescence indicate that i) radiative recombination occurs via the repopulation of *Chl(D1) itself; ii) non-radiative charge recombination reactions appeared to be faster in the T179H-PSII; and iii) the properties of PD1PD2 were unaffected by this mutation, and consequently iv) the immediate precursor state of the radiative excited state is the Chl(D1)(+)Pheo(D1)(-) radical pair. Chlorophyll bleaching due to high intensity illumination correlated with the amount of O-1(2) generated. Comparison of the bleaching spectra with the electrochromic shifts attributed to Chl(D1) upon Q(A)(-) formation, indicates that in the T179H-PSII and in the WT*3-PSII, the Chl(D1) itself is the chlorophyll that is first damaged by O-1(2), whereas in the T179V-PSII a more red chlorophyll is damaged, the identity of which is discussed. Thus, Chl(D1) appears to be one of the primary damage site in recombination-mediated photoinhibition. Finally, changes in the absorption of Chl(D1) very likely contribute to the well-known electrochromic shifts observed at similar to 430 nm during the S-state cycle.