The recent cloning of a gonadotrophin-releasing hormone receptor (GnRH-R) cDNA from rainbow trout showed that it contains several in-frame ATG codons, one of which, ATG2, corresponds to that found in other species. However, an upstream coclon, ATG1, could give rise to a protein with a larger extracellular domain. Using S1 nuclease assay and a method combining primer extension and RACE-PCR, we characterized a second population of mRNA, termed mRNA-2, with a distinct 5'untranslated region and lacking ATG1. The genomic origin of the two mRNAs was determined by establishing the complete gene structure, which shows, for the first time in a vertebrate species that an alternative splicing and promoter usage generate two GnRH-R mRNA variants whose 5' extremities are encoded by two different exons. The analysis of the tissue distribution indicated that mRNA-2 presents a broader pattern of expression and is detected at higher levels than mRNA-1. Interestingly, it was found that those two mRNAs are differentially expressed in male and female gonads during gametogenesis. In particular, the variations of mRNA-1 levels parallel those of sGnRH expression during spermatogenesis, indicating that tissue-specific processing of the GnRH-R mRNA may underlie the effects of GnRH as a paracrine/autocrine regulator of gonadal functions.