Neuropeptide Y (NPY) and cholecystokinin (CCK) play important roles in regulating appetite in vertebrates, including mammals and fish. Understanding the appetite mechanism is important in aquaculture to improve production performance. The yellowtail Seriola quinqueradiata is one of the most cultured fish in Japan, but little is known about its appetite hormones. In the present study, complementary DNA encoding for NPY was cloned in yellowtail and consists of 604 bp, in which deduced amino acid sequences show high identity to those of other teleosts. In tissue distribution, the npy and cck mRNAs were detected in all examined tissues (whole brain, telencephalon, optic tectum, hypothalamus, cerebellum, pituitary, retina, stomach, pyloric caeca, anterior intestine, liver, and kidney). In the fasting experiment, only npy mRNA expression in the hypothalamus responded to fasting, showing a significantly high value compared with that in control fish. The expression of cck mRNA in the examined tissues did not change with fasting. The npy mRNA expression in the hypothalamus might be involved in feeding regulation in yellowtail.