The medaka Oryzias latipes is a small freshwater fish native to Asia. It is now emerging as a promising model system for developmental, neural and reproductive research. Not only is the medaka embryo optically clear, it is also highly amenable to genetic manipulation and artificial control of reproduction. Furthermore, the medaka genome project has almost been completed, and much information has been accumulated on its reproductive physiology. We identified and characterized the medaka genes for the neuropeptide, gonadotropin-releasing hormone (gnrh), and its receptors (gnrhr), which plays crucial central roles in the control of reproduction. The medaka has three gnrh and three gnrhr genes, while most of tetrapods have less number of gnrh and gnrhr genes. Synteny analysis revealed that a gene duplication that gave rise to the third paralogous gnrh occurred before the divergence of teleosts and tetrapods and it has been lost only in the tetrapod lineage. We then generated transgenic medaka expressing green fluorescent protein under the control of the gnrh promoters to track the development of the gnrh neurons in vivo. Our images revealed that gnrh neurons in the ventral preoptic area and terminal nerve ganglion originated in the olfactory region, while the medial basal telencephalic gnrh neurons arose from the rostral telencephalon and the dorsal preoptic gnrh neurons migrate from the dorsal telencephalon. Using the transgenic medaka, we also found that kal1 and p73 are required for the migration and development of gnrh neurons. Further analysis using the medaka system will aid in the understanding of the neural control of reproductive function.