Abstract: To elucidate the role of intestinal fatty acid binding protein (Ifabp) in the regulation of lipids metabolism, unigenes were obtained from transcriptome of liver in spotted scat, Scatophagus argus. Two subtypes of ifabp genes (ssifabp2a and ssifabp2b) were isolated and analyzed in the female and male S. argus, respectively. Tissue distributions and changes of ssifabp2a and ssifabp2b in fast feeding and re-feeding were also observed. Phylogenetic tree results showed that ssIfabp2a was clustered with other Ifabp2a, Ifabp or IfabpX1, while ssIifabp2b was clustered with Ifabp2b or Ifabp-like in Osteichthyes. Homology analysis revealed that the sequence identity of ssifabp2a was 78.8%—87.9% with other Osteichthyes Ifabp2a, Ifabp or IfabpX1. The sequence identity of ssifabp2b was 79.5%—87.9% with other Osteichthyes Ifabp2b or Ifabp-like. The sequence identity was 73.5% between ssifabp2a and ssifabp2b. RT-PCR showed that ssifabp2a was the highest in intestine, and had a moderate level in kidney and liver. And ssifabp2b was also the highest in intestine, but had a moderate level in liver, stomach and hypothalamus in male. However, the expression of ssifabp2a was the highest in stomach, and moderate in kidney, liver and hypothalamus, with a weak expression level in other tissues and no expression in pituitary. The ssifabp2b was expressed strongly in hypothalamus, ovary, heart and intestine, and weakly in other tissues, but had no expression in gill of females. In the intestine, the expression of ssifabp2a decreased significantly, but there was no significant change of ssifabp2b after 2d of food deprivation. The expression of ssifabp2a decreased significantly compared with the control group, but there was no significant difference on the expression of ssifabp2b within the 7 day fasting group. The expressions of ssifabp2a and ssifabp2b increased significantly with refeeding 3-h after the scheduled feeding time. In liver, the expression of ssifabp2a was not changed, but the expression of ssifabp2b increased significantly after 2-day of food deprivation. However, the ssifabp2a and ssifabp2b were all increased during the 7-day fasting, and decreased significantly with refeeding 3-h after the scheduled feeding time. In summary, ssIfabp2a and ssIfabp2b are involved in the regulation of lipids metabolism at liver and intestine in Scatophagus argus.