To better understand the relation of UCP1,UCP2 to the physiology mechanism of Chinese perch (Siniperca chuatsi),UCP1,UCP2 gene sequence and exon/intron structure were obtained from Chinese perch by PCR and RACE method. Using βactin as external control, six tissues UCP1,UCP2 gene expression specificity of Chinese perch were also studied by RTPCR. The UCP1,UCP2 gene sequences were 3 146 bp, 2 890 bp in length. ORF were 942 bp, 939 bp and the deduced protein sequences are 313, 312 amino acids respectively.UCP1 included 5 introns and 6 exons and UCP2 has 7 introns and 8 exons. In the deduced amino acid sequence of UCP1,UCP2, three mitochondrial carrier protein motifs, the UCP signature motifs, six transmembrane αhelix domains and the putative purinenucleotide binding domain (PNBD) both were found. The UCP1 mRNA is primarily expressed in liver, and low level of expression can also be detected in intestine. The UCP1 mRNA was not detectable in spleen, muscle, brain and adipose tissue. In contrast, the UCP2 mRNA is ubiquitous in four selected tissues. The high abundance was observed in adipose tissue, muscle and intestine, and low abundance was observed in liver. Brain has no expression. The data indicated that tissue specificity of Chinese perch UCP1,UCP2 mRNA probably relates to their feed habits, physiology role, and mRNA expression level may be greatly affected by ROS production in different tissues.