It capitalizes on the portability of microbial opsins in efficiently coding for light sensation and effector function within a single gene, and the endogenous presence of the essential organic cofactor retinal in all vertebrate tissues tested, including brain. Thus, the single-component nature of the system is preserved, and no exogenous chemicals need to be added. Furthermore, neurons transduced with opsins are responsive to visible-spectrum light with biologically well-tolerated wavelengths and intensities. Also, the ability to deliver temporally precise light pulses to deep mammalian tissues in vivo with novel, engineered optical devices provides a great degree of experimental versatility. Together, these properties have triggered a surge of interest not only into immediate neuroscience applications, but also into using genomics and molecular engineering to expand the repertoire of tools and generate novel classes of functionality for neuroscience. Here we focus on the fundamentals of microbial opsin gene relationships and the structure–function properties of the ancient and powerful class of proteins encoded by these genes.