Ghrelin, glucagon-like peptide-1 (GLP-1), and peptide YY (PYY) are potent hormones mediating food intake according to the nutritional status in fish. However, limited information is available on these genes and their expression in response to nutrition in silver pomfret (Pampus argenteus). A comparison analysis revealed that ghrelin and GLP-1 were relatively conserved in marine fish. PYYa and PYYb shared a low identity and were clustered to different PYY branches. Ghrelin, pyya, and pyyb mRNAs were highly expressed in the brain, while glp-1 was highly expressed in the gills and liver. The ghrelin mRNA expression was relatively high an hour post-feeding and decreased after 3 to 72 h of fasting. The glp-1 mRNA expression was increased after 6 to 24 h of fasting. The pyya mRNA expression was increased after 72 h of fasting, while the pyyb expression remained stable during fasting. The diet with 14% lipid promoted the expressions of glp-1, pyya, and pyyb, but inhibited the ghrelin expression. The ghrelin expression in the intestine was increased after palmitic acid, oleic acid (OA), linoleic acid (LA), α-linolenic acid, eicosapentaenoic acid (EPA), and docosahexaenoic acid (DHA) incubation. OA decreased the expression of glp-1 and increased the expression of pyya. The expression of pyyb was downregulated by LA, DHA, and EPA. These results suggest the importance of ghrelin, glp-1, and pyy in coordinating food intake in response to fasting, dietary lipid concentration, and fatty acids in silver pomfret.