Gonadotropin-inhibitory hormone (GnIH) has been found to inhibit the synthesis and release of gonadotropin (GTH) in avian and mammalian species. It was originally identified in the brain of a quail as a novel hypothalamic neuropeptide with a C-terminal Arg-Phe-NH2 motif (RFamide peptide). Homologs of this peptide have been identified in a couple of model fish species such as goldfish (Carassius auratus) and zebrafish (Danio rerio). Understanding GnIH system could be particularly useful in some aquaculture species with problems of frequent reproduction and/or precautious sexual maturation. However, GnIH system in such species has not been studied yet. In this study, we have identified a pupative GnIH gene in the Nile tilapia (Oreochromis niloticus). We also investigated the role of GnIH in the reproduction of this species. The full length sequence of putative tilapia GnIH gene coded for a protein (197 amino acids) containing two modified RFamides (MPLRF and LSQRF) and a LPQRF cDNA sequence of 594 bp. This putative GnIH gene showed high homology with the GnIH genes of Takifugu rubripes (72%) and Tetraodon nigroviridis (74%). PCR analysis showed that expression of this gene was ubiquitously distributed in the whole brain, ovary and testis as well as in the peripheral tissues examined in this study (liver, kidney, intestine, spleen, muscle and gill) except heart and eye. Expression level of this gene in sexually inactive group was significantly higher than the expression level in first gonadal development and sexually active groups (P<0.05). On the contrary, the expression level of LH-β gene was low in sexually inactive group but significantly higher in first gonadal development and sexually active groups (P<0.05). However, no significant difference was observed in the level of FSH-β gene expression between different reproductive phases in this species. In vitro studies revealed an inhibitory effect of GnIH on LH-β mRNA and FSH-β mRNA levels. No significant difference between GnIH and GnIH with LHRH-a treatments on LH-β and FSH-β mRNA expression in female tilapia pituitary cells.