A halophilic archaeon, Halobacterium salinarum, exhibits phototactic behaviors, by which the organism is guided to red-orange light and evades shorter wavelengths of light. The phototaxis is mediated by two retinal proteins, sensory rhodopsin I and II (SRI and SRII), whose structures are analogous to the cognate protein bacteriorhodopsin, a light-driven proton pump. SRI mediates both attractant and repellent swimming behaviors to orange light and near- UV light, respectively. The two different signaling through the single photoreceptor have been ascribed to the presence of two active structures of SRI (S$\_$373/ and P$\_$520), which are produced upon orange light illumination of SRI and upon subsequent near-UV illumination of S$\_$373/, respectively. In the present study, we have measured the difference FTIR spectra of S$\_$373/ and P$\_$520/ states. In P$\_$520/, the isomeric structure of the chromophore is assignable to all-trans, and the Schiff base of the chromophore is protonated with concomitant deprotonation of Asp76, a combination which allows for the formation of a salt bridge between them. It was suggested that the way of interaction between the Schiff base and the counterion, which is different among SRI$\_$587/, S$\_$373/ and P$\_$520/ and which has been shown to drive the conformational changes in the cognate protein, bacteriorhodopsin, is the key to controlling conformational changes for the attractant and the repellent signaling by SRI.