This paper reports on the distribution, relationship and seasonal variations of neuropeptide Y (NPY)-like and gonadotropin-releasing hormone (GnRH)-like immunoreactants in the brain and hypophysis of the bony fish, the ayu Plecoglossus altivelis. NPY-like immunoreactivity was widely distributed in the brain: labeled cells were found in the nervus terminalis, the nucleus entopeduncularis, the habenula, the nucleus preopticus periventricularis, the nucleus tuberis lateralis, the mediodorsal hypothalamus, the dorsal tegmentum, and other sites. NPY fibers were considerably dense in the telencephalon and hypothalamus, and innervated the hypophysis. GnRH-positive cells occurred in the nervus terminalis and were sparsely distributed in the preoptic and tuberal areas of the hypothalamus. GnRH fibers were found in various regions of the brain. They were relatively dense in the hypothalamus, showing a local concentration in the middle region of the neurohypophysis. The GnRH-positive cells and fibers in the hypothalamo-hypophyseal complex increased in density around the spawning season. In tandem with gonadal maturation, NPY labeling in the cells of the nucleus tuberis lateralis became intense concomitantly with an increase in the labeled varicosities in the middle region of the neurohypophysis. Double immunostaining showed that NPY fibers were closely apposed to GnRH cells in the preoptic area. These results suggest a correlative involvement of NPY and GnRH in the control of the hypophyseal gonadotropic function of the ayu.