The biochemistry and circadian regulation of luminescence in two Pyrocystis species, P. lunula Hulburt and P. noctiluca Murray et Haeckel, were compared with a well-studied species, Gonyaulax polyedra Stein. All exhibit circadian rhythms and all have similar luciferins and luciferases. However, the Pyrocystis species lack a second protein involved in the reaction in Gonyaulax, the luciferin (substrate) binding protein, which sequesters the luciferin at the cytoplasmic pH and releases it upon acidification, thus controlling the characteristic flashing, which is similar in the three species. More striking is the difference in the circadian regulation of luminescence, which in Gonyaulax involves the daily synthesis and destruction of the two proteins, along with the luminous organelles (scintillons) from which light is emitted, and which are present in all species. In the Pyrocystis species, the amount of luciferase is the same in extracts made during the day and night phases; its circadian regulation in vivo may be attributed to a change in its localization from day to night phase.