At date, studies are beginning to show that ionotropic glutamate receptors (iGluRs) are influenced by the orexin/hypocretin (ORX) system during the regulation of several physiological functions in mammals. In this study, we showed that the effects of ORX-A and specific glutamatergic antagonists (3-(+)-2-carboxypiperazin-4-yl-propyl-1-phosphonate, CPP/cyano-7-nitro-quinoxaline-2,3-dione, CNQX) on the expression of NMDAR (NR1) and AMPAR (GluR2) subtype genes underlie a tight relationship of the ORXergic system with iGluRs in the teleost Carassius auratus (goldfish; Linnaeus, 1758). The application of specific primers for NR1 and GluR2 permitted us to identify two partial coding sequences (cds) of 115 bp and 90 bp that were highly similar (97% and 81%, respectively) to the related sequences of the rat (Rattus norvegicus). These cds were used to carry out a semi-quantitative RT-PCR (reverse transcription-polymerase chain reaction) in which a differentiated expression pattern of NR1 and GluR2 was obtained following drug treatments. Interestingly, goldfish treated with ORX-A showed a significant (p < 0.001) up-regulation of NR1 expression (∼120%) while GluR2 was only moderately up-regulated (+45%; p < 0.05) with respect to controls. As far as CPP effects were concerned, this NMDAR antagonist strongly blocked (-72%; p < 0.01) NR1 expression while CNQX did not account for any significant variation with respect to controls. Moreover, the contextual administration of ORX-A+CPP continued to provide a blocking effect on NR1 expression, especially when compared to ORX-A-treated fish (-98%). On the other hand, ORX-A+CNQX caused an up-regulated trend even though of a lesser extent with respect to ORX-A-treated fish (-44%). Regarding GluR2, only the AMPAR antagonist moderately blocked (-38%) its expression, an effect that was completely abolished in the presence of ORX-A. Overall, results of the present study highlight, for the first time, a prevalent up-regulatory role of ORX-A on NMDAR subtype mRNA expression in fish.