Photosystem II (PSII), an essential component of oxygenic photosynthesis, is a membrane-bound pigment protein complex found in green plants and cyanobacteria. Whereas the molecular structure of cyanobacterial PSII has been resolved with at least medium resolution [Zouni, A., Witt, H.-T., Kern, J., Fromme, P., Krauss, N., Saenger, W. & Orth, P. (2001) Nature (London) 409, 739-743; Kamiya, N. & Shen, J.R. (2003) Proc. Natl Acad. Sci. USA 100, 98-103], the structure of higher plant PSII is only known at low resolution. Therefore Fourier transform infrared (FTIR) difference spectroscopy was used to compare PSII from both Thermosynechococcus elongatus and Synechocystis PCC6803 core complexes with PSII-enriched membranes from spinach (BBY). FTIR difference spectra of T. elongatus core complexes are presented for several different intermediates. As the FTIR difference spectra show close similarities among the three species, the structural arrangement of cofactors in PSII and their interactions with the protein microenvironment during photosynthetic charge separation must be very similar in higher plant PSII and cyanobacterial PSII. A structural model of higher plant PSII can therefore be predicted from the structure of cyanobacterial PSII.