Samples of proteorhodopsin expressing bacteria have been obtained from the Eastern Pacific Ocean, Central North Pacific Ocean and Southern Ocean, Antarctica. Subsequently, genes of proteorhodopsin variants have been identified in samples from the Mediterranean, Red Seas, the Sargasso Sea, and Sea of Japan, and the North Sea.
Proteorhodopsin variants are not spread randomly, but disperse along depth gradients based on the maximal absorption-tuning of the particular holoprotein sequence; this is mainly due to the electromagnetic absorption by water which creates wavelength gradients relative to depth. Oxyrrhis marina is a dinoflagellate protist with green-absorbing proteorhodopsin (a result of the L109 Group) that exists mostly in shallow tide pools and shores, where green light is still available. Karlodinium micrum, another dinolagelate, expresses a blue tuned proteorhodopsin (E109) which may be related to its deep water vertical migrations.  O. marina was originally believed to be a heterotroph, however the proteorhodopsin may well partake in a functionally significant manner, as it was the most abundantly expressed nuclear gene and, furthermore, is dispersed unevenly in the organism, suggesting some organelle membrane function.  Previously the only known eukaryotic solar energy transducing proteins were Photosystem I and Photosystem II. It has been hypothesized that lateral gene transfer is the method by which proteorhodopsin has made its way into numerous phyla.  Bacteria, archaea and eukarya all colonize the photic zone where they come to light; Proteorhodopsin has been able to disseminate through this zone, but not to other portions of the water column.