The excitation intensity dependence of the kinetics of the primary processes and of the yield of radical pair formation in the isolated D1-D2-cyt-b559 reaction center of photosystem II has been studied by femtosecond transient absorption spectroscopy. It is shown that the kinetics is strongly dependent on the excitation intensity. The radical pair yield as a function of excitation intensity is compared with the theoretical annihilation curve and a good agreement between theory and experiment is observed, indicating that the intensity effects on the kinetics and radical pair yield arise primarily from annihilation processes. Sufficiently annihilation-free measurements require excitation intensities that give rise to less than or equal to 0.06 absorbed photons/RC while maintaining a high signal/noise ratio of greater than or equal to 100:1 at most detection wavelengths in order to resolve the complex kinetics. It is shown that such low excitation intensities give rise to absorption changes that are at the edge of the capabilities of present femtosecond absorption equipment. We also compare the excitation conditions that have been used so far by other research groups for published transient absorption data on the isolated D1-D2-cyt-b559 complex. This comparison shows that essentially all published data have been obtained under conditions where annihilation or quenching effects are expected to significantly distort the kinetics and time-resolved spectra and to reduce the radical pair yield.