In this study we examined the spatial relationship of GABA-containing and GnRH-containing neurons by immunocytochemistry and in situ hybridization in larval and adult brains of sea lamprey, Petromyzon marinus. In immunocytochemical studies, GABA-containing neurons were detected early in lamprey development, by day 20 post-fertilization. At this time point, one population of GABA-containing neurons was visualized in the hypothalamus and preoptic area, and another population was located in the olfactory bulb of the telencephalon. By day 30 after fertilization, after the GABA neurons were detected, GnRH-containing neurons were visualized in the preoptic area/rostral hypothalamus region, adjacent to the GABA-containing neurons in the wall of the third ventricle. Similarly, in adult lamprey brains distinct populations of both GABA- and GnRH-containing neurons were located in the hypothalamus adjacent to the third ventricle. To further establish a proximate relationship between GABA and GnRH, the mRNA for glutamate decarboxylase (GAD), the enzyme catalyzing GABA synthesis from glutamate, and GnRH were examined by in situ hybridization in the brains of larval lamprey. These studies also showed that GnRH and GAD are produced in cell populations in and around the third ventricle of the hypothalamus. This close spatial relationship of GABA neurons and GnRH neurons provides a basis for a regulatory role of GABA on GnRH neurons in the sea lamprey.