Enzymes with multiple catalytic sites are rare, and their evolutionary significance remains to be established. This study of luciferases from seven dinoflagellate species examines the previously undescribed evolution of such proteins. All these enzymes have the same unique structure: three homologous domains, each with catalytic activity, preceded by an N-terminal region of unknown function. Both pairwise comparison and phylogenetic inference indicate that the similarity of the corresponding individual domains between species is greater than that between the three different domains of each polypeptide. Trees constructed from each of the three individual domains are congruent with the tree of the full-length coding sequence. Luciferase and ribosomal DNA trees both indicate that the Lingulodinium polyedrum luciferase diverged early from the other six. In all species, the amino acid sequence in the central regions of the three domains is strongly conserved, suggesting it as the catalytic site. Synonymous substitution rates also are greatly reduced in the central regions of two species but not in the other five. This lineage-specific difference in synonymous substitution rates in the central region of the domains correlates inversely with the content of GC 3, which can be accounted for by the biased usage toward C-ending codons at the degenerate sites. RNA modeling of the central region of the L. polyedrum luciferase domain suggests a function of the constrained synonymous substitutions in the circadian-controlled protein synthesis.codon bias ͉ domain duplication ͉ synonymous substitutions T he luciferase (LCF) of the bioluminescent dinoflagellate Lingulodinium polyedrum (Lp; formerly Gonyaulax polyedra) has three homologous tandemly arranged 377-aa-long domains, each of which is catalytically active (1). The LCF of another dinoflagellate, Pyrocystis lunula (Pl), has a similar structure (2). In both, we found the amino acids in the central region of each of the three domains to be highly conserved intramolecularly at Ϸ95% identity, compared with Ϸ65% in the flanking regions. Remarkably, and only in Lp, there were fewer synonymous substitutions in the central region.These results are intriguing from both evolutionary and mechanistic viewpoints. To grasp their significance, we investigated the LCFs of five other bioluminescent dinoflagellates, all of which are photosynthetic: Alexandrium affine (Aa), Alexandrium tamarense (At), Pyrocystis fusiformis (Pf ), Pyrocystis noctiluca (Pn), and Protoceratium reticulatum (Pr). All were shown to have the same basic configuration, i.e., tandem triplication of catalytic domains following an Ϸ110-aa-long N-terminal sequence. Fortuitously, it turned out that Lp and Pl LCFs represent extremes of a spectrum of LCF structures with regard to synonymous substitution rates in the central region of each domain.Bioluminescence in dinoflagellates has been well characterized only in Lp, where the three components involved in light emission are packaged together in unique cellular organelles,...