We have achieved a major breakthrough since we have experimentally elucidated how cofactor geometries play roles on the electronic interaction of photoinduced primary charge-separated (CS) states in the photosystem II reaction center (PSII RC) of a higher plant that undergoes the water splitting. Using a time-resolved EPR method, we have herein clarified both the molecular geometry and the electronic coupling of the CS in the PSII RC. A highly localised hole distribution at PD1+ which is essential in oxidizing Mn4CaO5 has been demonstrated in the primary CS state. A weak electronic coupling between PD1+ and PheoD1- is explained by a limited spin density at the terminal vinyl group in PheoD1, regulating an orbital overlap to inhibit unwanted recombination. To our knowledge, this is the first study that has revealed molecular mechanism of the efficient generation of the initial oxidative radical pairs by characterising both the geometries and the electronic interaction in the higher plant. Above fundamental characteristics of the primary CS state are essential keys to the artificial light-energy conversion systems and also are highly informative for understanding the evolutions of the molecular engineering in the higher plants.