Halorhodopsin (HR) is a light-driven chloride pump. Cl- is bound in the Schiff base region of the retinal chromophore, and unidirectional Cl-transport is probably enforced by the specific hydrogen-bonding interaction with the protonated Schiff base and internal water molecules. It is known that HR from Natronobacterium pharaonis (pHR) also pumps NO3- with similar efficiency, suggesting that NO3- binds to the Cl--binding site. In the present study, we investigated the properties of the anion-binding site by means of ultrafast pump-probe spectroscopy and low-temperature FTIR spectroscopy. The obtained data were surprisingly similar between pHR-NO3- and pHR-Cl-, even though the shapes and sizes of the two anions are quite different. Femtosecond pump-probe spectroscopy showed very similar excited-state dynamics between pHR-NO3- and pHR-Cl-. Low-temperature FTIR spectroscopy of unlabeled and [zeta-N-15]Lys-labeled pHR revealed almost identical hydrogen-bonding strengths of the protonated retinal Schiff base between pHR-NO3- and pHR-Cl-, which is similarly strengthened after retinal isomerization. There were spectral variations for water stretching vibrations between pHR-NO3- and pHR-Cl-, suggesting that the water molecules hydrate each anion. Nevertheless, the overall spectral features were similar for the two species. These observations strongly suggest that the anion-binding site has a flexible structure and that the interaction between retinal and the anions is weak, despite the presence of an electrostatic interaction. Such a flexible hydrogen-bonding network in the Schiff base region in HR appears to be in remarkable contrast to that in light-driven proton-pumping proteins.