pharaonis phoborhodopsin (ppR; also called pharaonis sensory rhodopsin II, psR-II) is a photoreceptor for negative phototaxis in Natronomonas pharaonis. ppR activates the cognate transducer protein, pHtrII, upon absorption of light.  ppR and pHtrII form a tight 2:2 complex in the unphotolyzed state, and the interaction is somehow altered during the photocycle of ppR.  We have studied the signal transduction mechanism in the ppR/pHtrII system by means of low-temperature Fourier-transform infrared (FTIR) spectroscopy.  In the study, spectral comparison in the absence and presence of pHtrII provided fruitful information in atomic details, where vibrational bands were identified by use of isotope-labeling and site-directed mutagenesis. We revealed that retinal isomerization strengthens hydrogen bond of the O-H group of Thr204 in ppR, which takes place only in the presence of pHtrII.  Such structural perturbation is restored in the M intermediate, while the hydrogen bond of Asn74 in pHtrII is altered.  Temperature dependence on the amide-I vibration in ppR suggests the presence of multiple M states during the activation process, which is disrupted by the mutation of Gly83 in pHtrII.  This suggests the importance of dynamical motion of the cytoplasmic domain in the protein-protein interaction. We established the two pathways of light signal conversion from the receptor to the transducer; (i) from Lys205 (retinal) of ppR to Asn74 of pHtrII through Thr204 and Tyr199, and (ii) from Lys205 of ppR to the cytoplasmic loop region of pHtrII that links Gly83.