'bacteriorhodopsin' originates as a modern scientific compound formed from the combining form 'bacterio-' (from Greek 'bakterion' meaning 'small rod') and 'rhodopsin' (from Greek 'rhodon' meaning 'rose'—referring to color—and 'opsin' meaning 'appearance' or a type of protein pigment).

'bacteriorhodopsin' was coined in the 20th century after the discovery of a retinal-binding, light-driven protein in halophilic microorganisms; it was formed by combining 'bacterio-' + 'rhodopsin' (the latter name originally used for the visual pigment) and came into use in microbiology and biochemistry literature from the 1960s–1970s onward.

Initially conceived as a 'bacterial rhodopsin' to indicate similarity to visual rhodopsin, the term has come to denote this specific archaeal (historically described alongside bacteria) membrane protein that functions as a light-driven proton pump.