Proteorhodopsin (pR) is a bacteriorhodopsin (bR) homologue, recently discovered in oceanic bacterioplankton, which functions as a light-driven proton pump. Resonance Raman spectra of pR excited with 532-nm light indicate that there are two subpopulations of pR within the sample solubilized in octylglucoside detergent and maintained in a light-adapted state in a spinning Raman cell. The subpopulations exhibit two distinct chromophore environments, as evidenced by two sets of split peaks, 1642/1655 cm(-1) (corresponding to the Schiff base nu(C=N) vibration) and 1244/1252 cm(-1) (corresponding to a retinylidene-lysine N-C-H rock). These populations most likely arise either from different post-translational modifications of the heterologously expressed protein or from a mixture of retinal isomers (all-trans and 13-cis) that was previously reported to be present in light-adapted pR in a 60:40 ratio. However, the latter possibility seems at odds with the resonance Raman fingerprint spectral patterns in both natural-abundance and 15-H-2-retinal-subsituted pR, which are consistent with an all-trans chromophore configuration similar to that of light-adapted bR.