We report that Triton X-100 can alter the temporal sequence of the light-induced proton uptake and release of archaerhodopsin 4 (AR4), a proton pumping protein in a species of Halobacteria from a Tibetan salt lake. Under physiological conditions, AR4 isolated from the bacterium exhibits a reversed temporal order of proton release and uptake compared to what is observed for bacteriorhodopsin (BR). However, in the presence of Triton X-100 early proton release was observed in AR4 at neutral pH by us. Further, this temporal order for light-driven proton release and uptake for AR4 was found to be recovered after the removal of Triton X-100 by Biobeads. This phenomenon of detergent-induced alteration of the order of proton release and uptake has not yet been reported in any other retinal-containing membrane protein such as BR. Our findings indicate that the function of AR4 is influenced by its self-assembled state, and meanwhile imply some subtle protein-lipid interactions or protein-protein interactions in adjusting the proton pumping behavior of AR4.