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We have studied the structural changes induced by optical excitation of the chromophore in wild-type photoactive yellow protein (PYP) in liquid solution with a combined approach of polarization-sensitive ultrafast infrared spectroscopy and density functional theory calculations. We identify the νC₈−C₉ marker modes for solution phase PYP in the P and I₀ states, from which we derive that the first intermediate state I₀ that appears with a 3 ps time constant can be characterized to have a cis geometry. This is the first unequivocal demonstration that the formation of I₀ correlates with the conversion from the trans to the cis state. For the P and I₀ states we compare the experimentally measured vibrational band patterns and anisotropies with calculations and find that for both trans and cis configurations the planarity of the chromophore has a strong influence. The C₇C₈−(C₉O)−S moiety of the chromophore in the dark P …