Microflora in fish digestive tract play important roles in digestion, absorption, immunity and organ development. In this study, terminal restriction fragment length polymorphism (T-RFLP) technique was employed to examine the changes in structure of the intestinal microbiota of L. japonicus after fasting and refeeding. The results showed that microflora structure of Lateolabrax japonicus intestinal wall changed after 2 weeks of fasting. The main T-RFs that caused the microflora structure differences among fasting group, refeeding groups and control groups were T-RFs 496 bp, 437 bp, 450 bp and 155 bp.Especially, after 2 weeks of fasting, the relative abundance of T-RF 496 bp (Escherichia) reduced to 21.25%±9.97% from 43.11%±3.95% of the beginning (C0) and the bacterial diversity index (H', E' and 1/D) of intestinal wall increased significantly compared with control groups. Bacterial diversity index (H', E' and 1/D) of intestinal wall were decreased and the microflora structure was recovered gradually with the refeeding. Meanwhile, the relative abundance of T-RF 496 bp gradually increased to 55.49%±8.37%.The results also indicated that the microflora structure of intestinal walls was different from that of intestinal contents, but their main phyla were the same, namely, Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes.