The reversible photoswitching of the photochromic fluorescent protein Padron0.9 involves a cis-trans isomerization of the chromophore. Both isomers are subjected to a protonation equilibrium between a neutral and a deprotonated form. The observed pH dependent absorption spectra require at least two protonating groups in the chromophore environment, modulating its proton affinity. Using femtosecond transient absorption spectroscopy, we elucidate the primary reaction steps of selectively excited chromophore Speties. Employing kinetic and spectral modeling of the dine dependent transients, we identify intermediate states and their spectra. Excitation of the deprotonated trans species is followed by excited state relaxation and internal conversion to a hot ground, state on a time scale of 1.1-6.5 ps. As the switching yield is very low (Phi(trans -> cis) = 0.0003 +/- 0.0001), direct formation of the cis isomer in the time-resolved experiment is not observed. The reverse switching route involves excitation of the neutral cis chromophore.. A strong H/D isotope effect reveals the initial reaction step to be an excited State proton transfer with a rate constant of k(H) = (1.7 ps)(-1) (k(D) = (8.6 ps)(-1)) competing with internal conversion (k(ic) = (4.5 ps)(-1)). The deprotonated excited cis intermediate relaxes to the well-known long-lived fluorescent species (k(r) = (24 ps)(-1)). The switching quantum yield is determined to be low as well, Phi(cis -> trans) = 0.02 +/- 0.01. Excitation of both the neutral and deprotonated cis chromophores is followed by a ground state proton transfer reaction partially re-establishing the disturbed ground state equilibrium within 1.6 ps (deuterated species: 5.6 ps). The incomplete equilibration reveals an inhomogeneous population of deprotonated cis species which equilibrate on different time scales.