In this study, the authors examine the effects of chloride and protons on the chromophores of halorhodopsin and bacteriorhodopsin, with the expectation that these ions, substrates of the two light-driven pumps, respectively, will interact with the apoproteins sufficiently to perturb the retinal moiety. All experiments were with cell envelope vesicles at high salt concentrations, which preserved transport activity, i.e., either in 4 M NaCl or in 1.5 M Na sub(2)SO sub(4) with added NaCl. They find that in contrast with the photocycle of bacteriorhodopsin, whose major kinetic component shows sharp pH dependence, the flash-induced absorbance changes in halorhodopsin are virtually independent of pH between 5 and 9. Chloride, on the other hand, which does not affect bacteriorhodopsin under these conditions, has profound effects on the photocycle of halorhodopsin: after addition of chloride, the flash yield for halorhodopsin is greatly enhanced, and the time for recovery from flash bleaching is increased about 4-fold.