Phosphoenolpyruvate carboxykinase (PEPCK) is known to exist as mitochondrial (PEPCK-M) and cytosolic isoforms (PEPCK-C). They are involved in glucose production and play vital roles in regulating glucose homeostasis. This study aimed to (1) clone and characterize PEPCK-C cDNA from golden pompano fish (Trachinotus ovatus), which are known to have poor utilization of dietary carbohydrates, and (2) analyze the regulation of its expression by varying dietary carbohydrate-to-lipid ratios and nutritional status. A full length golden pompano PEPCK-C cDNA fragment of 2,652 bp was cloned, which contains an open reading frame of 1,875 bp encoding 624 amino acids and shows a high homology to cobia (Rachycentron canadum) PEPCK-C sequence (92% similarity). The analysis of tissue distributions of PEPCK-C mRNA showed that a high abundance of PEPCK-C was expressed in golden pompano liver, followed by kidney; while lower expression levels were found in the heart and intestine. In liver, PEPCK is under the regulation of dietary composition and nutritional status at the enzymatic and molecular levels. Our results indicate that PEPCK-C plays a modulating role in the adaptation of hepatic gluconeogenesis to different nutrient conditions. Thus, the absence of molecular inhibition of gluconeogenic PEPCK gene expression in rainbow trout (Oncorhynchus mykiss) and gilthead sea bream (Sparus aurata), which can at least partially account for their poor utilization of dietary carbohydrate, is specific to these species and is not observed in golden pompano. Further studies that examine, at the enzymatic and molecular levels, other key enzymes involved in hepatic glucose metabolism are necessary to understand the poor utilization of carbohydrates in golden pompano.