Melanin concentrating hormone (MCH) is well known as an orexigenic neuropeptide in mammals. Although there are two types of MCH receptor (MCH1R and 2R), there is few information about the function of MCH2R, because this receptor gene is lost in rodent. In this study, to consider the evolutionarily conserved function of MCH receptors, we examined the distribution of MCH1R and 2R expressing cells in the brain of a basal actinopterygian fish, Polypterus senegalus, that is located in the phylogenetic branch of fishes and tetrapod. We cloned MCH receptor cDNAs from P. senegalus and characterized phylogenetically. According to phylogenetic tree of MCH receptors, P. senegalus has MCH1R and 2R that are close to mammalian receptors. To investigate these mammal-like MCH1R and 2R expressing cells, we performed in situ hybridization. These receptor mRNAs were detected in the olfactory bulb, the telencephalon, the diencephalon, the rhombencephalon, and the spinal cord of P. senegalus. Especially, neurons of the habenular nucleus, the optic tectum, and the paraventricular organ showed strong signal for MCH1R mRNA. On the other hand, MCH2R mRNA expression was prominent in the pallium of telencephalon. These findings suggest that MCH1R and 2R are contributed to various and different central neural functions in this fish.