Microbial rhodopsins, also known as bacterial rhodopsins, are retinal-binding proteins that provide light-dependent ion transport and sensory functions in halophilic and other bacteria. They are integral membrane proteins with seven transmembrane helices, the last of which contains the attachment point (a conserved lysine) for retinal. Most microbial rhodopsins pump inwards, however "mirror rhodopsins" which function outwards have been discovered.

This protein family includes light-driven proton pumps, ion pumps and ion channels, as well as light sensors. For example, the proteins from halobacteria include bacteriorhodopsin and archaerhodopsin, which are light-driven proton pumps; halorhodopsin, a light-driven chloride pump; and sensory rhodopsin, which mediates both photoattractant (in the red) and photophobic (in the ultra-violet) responses. Proteins from other bacteria include proteorhodopsin.

As their name indicates, microbial rhodopsins are found in Archaea and Bacteria, and also in Eukaryota (such as algae) and viruses; although they are rare in complex multicellular organisms.

Rhodopsin was originally a synonym for "visual purple", a visual pigment (light-sensitive molecule) found in the retinas of frogs and other vertebrates, used for dim-light vision, and usually found in rod cells. This is still the meaning of rhodopsin in the narrow sense, any protein evolutionarily homologous to this protein. In a broad non-genetic sense, rhodopsin refers to any molecule, whether related by genetic descent or not (mostly not), consisting of an opsin and a chromophore (generally a variant of retinal). All animal rhodopsins arose (by gene duplication and divergence) late in the history of the large G-protein coupled receptor (GPCR) gene family, which itself arose after the divergence of plants, fungi, choanoflagellates and sponges from the earliest animals. The retinal chromophore is found solely in the opsin branch of this large gene family, meaning its occurrence elsewhere represents convergent evolution, not homology. Microbial rhodopsins are, by sequence, very different from any of the GPCR families.

The term bacterial rhodopsin originally referred to the first microbial rhodopsin discovered, known today as bacteriorhodopsin. The first bacteriorhodopsin turned out to be of archaeal origin, from Halobacterium salinarum. Since then, other microbial rhodopsins have been discovered, rendering the term bacterial rhodopsin ambiguous.

Below is a list of some of the more well-known microbial rhodopsins and some of their properties.

The ion-translocating microbial rhodopsin (MR) family ("TC# 3.E.1". Transporter Classification Database (tcdb.org).) is a member of the TOG Superfamily of secondary carriers. Members of the MR family catalyze light-driven ion translocation across microbial cytoplasmic membranes or serve as light receptors. Most proteins of the MR family are all of about the same size (250-350 amino acyl residues) and possess seven transmembrane helical spanners with their N-termini on the outside and their C-termini on the inside. There are nine subfamilies in the MR family:

A phylogenetic analysis of microbial rhodopsins and a detailed analysis of potential examples of horizontal gene transfer have been published.