Photoactive yellow protein (PYP) is a small cytosolic photoreceptor that actuates the negative phototactic response in its host organism Halorhodospira halophila. It has an optical absorption maximum at 446 nm (blue light). We report an initial study of the photocycle of PYP at the single molecule level using “high enhancement factor” surface-enhanced Raman scattering (SERS)-active nanostructures with 514 nm laser excitation. The SERS-active “nanometal-on-semiconductor” structures are prepared employing a redox technique on thin germanium films, coated on glass slides. Single molecule spectra are observed in terms of sudden appearance of discernable Raman peaks with spectral fluctuations. The single molecule spectra capture protonation, photo-isomerization, and H-bond breaking - the steps that are instrumental in the photocycle of PYP. This is indicative of single PYP molecules diffusing to high-enhancement-factor SERS sites, and undergoing photo-cycle under 514 nm excitation.