Recent studies have shown that there are multiple genes encoding gonadotropin-releasing hormone receptor (GnRH-R) in single species. In salmonids, however, only a single gene has been identified in the rainbow trout. We therefore isolated partial cDNAs from the brain and the pituitary of masu salmon Oncorhynchus masou by reverse transcription-polymerase chain reaction and 5′-rapid amplification of cDNA ends, using primers corresponding to conserved transmembrane domains (TMs). Five different partial cDNAs were isolated from an individual and termed as msGnRH-R1, R2, R3, R4 and R5. They are divided into two groups, msGnRH-R1, R2, R3 and msGnRH-R4, R5. Two groups share 59-71% nucleotide sequence identities. Phylogenetic analysis showed that the former group is closely related to the goldfish GnRH-R GfA, and the latter to GfB. All five msGnRH-R genes were expressed in the brain and msGnRHR1, R3 and R5 were expressed in the pituitary. In addition, we found mRNA for msGnRH-R1 in the kidney and ovary, and R2 in the ovary, whereas msGnRH-R5 gene was widely expressed in the muscle, heart, kidney and testis. Differences in the expression of msGnRH-R genes between maturing and spawning fish were observed in the brain and pituitary, except for the constantly expressed msGnRH-R5. A splicing variant of msGnRH-R1 mRNA that is capable of generating a truncated GnRH-R that consists of 5TMs was also expressed in the brain, pituitary and kidney. These results indicate that five different types of putative GnRH-R gene are present and expressed in the brain of masu salmon.