As a first step towards understanding the regulatory mechanisms underlying the asynchronous oogenesis in repetitive spawning fish, full-length cDNAs encoding the receptors for follicle stimulating hormone (FSH-R) and luteinizing hormone (LH-R) were isolated from the gonads of the flatfish Atlantic halibut (Hippoglossus hippoglossus). The predicted halibut FSH-R and LH-R of 664 and 698 amino acids, respectively, both contain the characteristic features of a large extracellular (EC) domain, a hepta-helical transmembrane (TM) domain, and a short cytoplasmic C-terminal tail. Halibut FSH-R and LH-R share only 42% overall sequence identity mostly due to low homology in the ligand-binding EC domain. Both receptors show high sequence identity to their orthologs of Nile tilapia, but seem to be more remotely related to the receptors in catfish, zebrafish and salmonids. In contrast to the intron-less TM domain of almost all vertebrate gonadotropin receptors, three introns were identified in this domain of halibut FSH-R, thus resembling the gene structure of Drosophila glycoprotein hormone receptor type I. The FSH-R pre-mRNA was shown to be processed in alternative ways by isolating two different transcripts encoding the complete receptor and four alternative spliced transcripts encoding different truncated receptor variants. Based on the DNA sequence variation and chromosomal organization of the gonadotropin receptors in several teleosts, we propose that the encoding genes have been duplicated in the fish lineage.