In order to improve our understanding of melatonin signaling, we have reviewed and revised the evolutionary history of melatonin receptor genes () in vertebrates. All gnathostome have a conserved gene organization with two exons, except for paralogs of some teleosts that show intron gains. Phylogeny and synteny analyses demonstrate the presence of four subtypes, MTNR1A, MTNR1B, MTNR1C, MTNR1D that arose from duplication of an ancestral during the vertebrate tetraploidizations (1R and 2R). In tetrapods, was lost, independently, in mammals, in archosaurs and in caecilian amphibians. All four subtypes were found in two non-teleost actinopterygian species, the spotted gar and the reedfish. As a result of teleost tetraploidization (3R), up to seven functional genes could be identified in teleosts. Conservation of the 3R-duplicated paralogs differs among the teleost lineages. Synteny analysis showed that the was conserved as a singleton in all teleosts resulting from an early loss after tetraploidization of one of the teleost 3R and salmonid 4R paralogs. Several teleosts including the eels and the piranha have conserved both 3R-paralogs of , and . Loss of one of the 3R-paralogs depends on the lineage: was lost in euteleosts whereas was lost in osteoglossomorphs and several ostariophysians including the zebrafish. We investigated the tissue distribution of expression in a large range of tissues in medaka. The medaka has conserved the four vertebrate paralogs, and these are expressed in brain and retina, and, differentially, in peripheral tissues. Photoperiod affects expression levels in a gene-specific and tissue-specific manner. This study provides new insights into the repertoire diversification and functional evolution of the gene family in vertebrates.