Abstract: Small peptide transporter (PepT1) is a transporter with low-affinity and high capacity peptide, which plays an important role in the peptide absorption. In order to reveal the molecular mechanism of the small peptide transporter PepT1-mediated protein digestion and absorption, the small peptide transporter PepT1 gene of the Siniperca chuatsi was cloned by using RT-PCR and RACE techniques. The full-length cDNA sequence of the PepT1 was 2480 bp, including 43 nucleotides at 5'UTR and 232 nucleotides at 3UTR and 2205 nucleotides as an open reading frame encoding a 735-amino-acid peptide. The PepT1 amino acid sequence was determined and it shared a similarity to those of other mammalian homolog protein, which included 12 helix trans-membrane regions and existed a large outer-ring between 9th and 10th of the transmembrane region. Homologous analysis of the PepT1 showed that the amino acid of the PepT1 was highly homologous to those of other vertebrates and it showed high percentages of similarities at 89% with Epinephelus aeneus and Dicentrarchus labrax. In addition, the PepT1 amino acid sequence varied in similarity to other vertebrates from 46% to 56%. The encoded protein molecular weight was predicted at 64.8 kD with pI at 8.97. The quantitative RT-PCR analysis demonstrated that the foregut and midgut may be the key parts of intestinal absorption of small peptides as the PepT1 expression in the foregut and midgut was significantly higher than the hindgut (P0.05). The PepT1 gene expression was detected in all post-embryonic developmental stages, and it showed a peak expression the growing to about 10g in weight, then the expression remained stable in late developmental stages. The significance of the work first reported the PepT1 cDNA structure and its expression pattern, furthermore, it provided a valuable reference for research on fish nutrition and physiology.