GnRH is a neuropeptide which plays an essential role in the control of reproductive fitness for all vertebrates. Increasing evidence suggests that multiple forms of GnRH may exist in most vertebrate brains. Southern blot analysis of the three GnRHs known to be present in perciform fish, the seabream (sb)GnRH, the salmon(s) GnRH and the chicken (c) GnRH-II, demonstrates that each is present as a single gene copy in the genome of the striped bass, Morone saxatilis. In order to investigate the physiological consequences of multiple GnRHs in a single vertebrate species, we have isolated and characterized two of the GnRH genes, those for sbGnRH and cGnRH-II. Computer analysis of 3.5 kb of sequence upstream of the sbGnRH gene reveals a number of consensus DNA binding sites which implicate steroids, such as estrogen and glucocorticoids, and the steroidogenic transcription factor, SF-1, as being involved in the regulation of sbGnRH gene expression. Sequence analysis of the cGnRH-II gene reveals evidence of multiple promoters. Expression studies using (1) solution hybridization-RNAse protection mapping with several RNA probes directed at various regions of the proGnRH gene, (2) primer extension assays using two specific oligonucleotide primers, and (3) reverse transcription PCR with several oligonucleotide primers on cGnRH-II transcripts demonstrate that the cGnRH-II gene initiates transcription at numerous sites using a TATA-less promoter within the brains of sexually mature striped bass. This study is the first to characterize and compare the promoter structures of two GnRH genes present in a single vertebrate species.