A structure-based approach to the mechanism of ion pumping in bacteriorhodopsin (BR) has fostered new hypotheses for the detailed molecular changes that underlie ion transport in this light-driven pump. Isomerization of the retinal from all-trans to 13-cis in response to absorption of the energy of a photon is thought to lead to proton transfer from the initially protonated Schiff base to an anionic aspartate residue (Asp85) in the first half of the BR photocycle. In this traditional view the proton is transferred directly from the Schiff base to Asp85. A comparison of structures of photocycle intermediates trapped shortly after proton transfer to Asp85 to those of the resting state suggested an alternative view for the mechanism of proton transfer. In this scenario, a local water molecule in hydrogen bond contact with the Schiff base and Asp85 in the resting state is destabilized upon isomerization of the retinal. The destabilized water loses a proton to Asp85 and the remaining hydroxyl anion migrates toward the positively charged Schiff base to abstract its proton. This mechanism, in which a hydroxyl ion is pumped in lieu of a proton, has now been challenged by interpretations of new structures for photointermediates that immediately precede and follow the deprotonation/protonation reaction. However, in contrast to the older structures in which photointermediates were prepared at room temperature, the new structures were obtained by illuminating wild-type BR in frozen crystals. The results of spectroscopic studies of BR suggest that the structures of intermediates trapped at low temperature may not be the same as native photocycle intermediates at room temperature. The precise mechanism of ion transfer in BR is therefore unresolved.