Time-resolved resonance Raman spectra of the hRL intermediate of halorhodopsin have been obtained. The structurally sensitive fingerprint region of the hRL spectrum is very similar to that of bacteriorhodopsin's L550 intermediate, which is known to have a 13-cis configuration. This indicates that hRL contains a 13-cis chromophore and that an all-trans----13-cis isomerization occurs in the halorhodopsin photocycle. hRL exhibits a Schiff base stretching mode at 1644 cm-1, which shifts to 1620 cm-1 in D2O. This demonstrates that the Schiff base linkage to the protein is protonated. The insensitivity of the C-C stretching mode frequencies to N-deuteriation suggests that the Schiff base configuration is anti. The 24 cm-1 shift of the Schiff base mode in D2O indicates that the Schiff base proton in hRL has a stronger hydrogen-bonding interaction with the protein than does hR578.