Transposable elements are major constituents of eukaryote genomes and have a significant effect on genome structure and stability. They also contribute to the genetic diversity and evolution of organisms. Knowledge of their distribution among several genomes is an essential condition to study their dynamics and to better understand their role in species evolution. Long terminal repeat (LTR)-retrotransposons have been reported in diverse eukaryote species, indicating a ubiquitous distribution. Among retrotransposons, the transposable element (TE) class, which are specific to eukaryotes, transpose via an RNA intermediate. Based on their structure, LTR-retrotransposons have been divided into two classes:ty3-gypsy and ty1-copia. In previous research, we found a ty3-gypsy-like retrotransposon, named JRE, in the genome of Jian carp, . To investigate the function of JRE in the genome of Jian carp, PCR amplification, fluorescence quantitative PCR and fluorescent in situ hybridization were used to explore the structure and characteristics of JRE retrotransposon. Multiple alignments of DNA and protein sequences were constructed using MEGA 5.0 software and were manually curated using BioEdit. Pairwise distances were estimated using the option pairwise deletion of gaps in MEGA5.0. The full-length JRE retrotransposon is 5126 bp, which includes two LTRs of 470 bp at the 5' end and 453 bp at the 3' end, and two open reading frames (ORFs) between them. One ORF of 4203 bp encodes the group-specific antigen (). The pol gene has a typical Ty3/gypsy retrotransposon structure, and the gene order is protease, reverse transcriptase, RNase H, and integrase (PR-RT-RH-IN). A phylogenetic analysis of the pol gene showed that it has similarities of 40.7%, 40%, 32.8%, and 30.1% to retrotransposons of the Yesso scallop, Farrer's scallop, a Great Barrier Reef sponge, and the spot swordtail fish, respectively. Therefore, JRE might belong to the JULE retrotransposon family. The copy number of the JRE retrotransposon in the genome of the Jian carp is 124, as determined by real-time quantitative PCR. The mRNA of the JRE retrotransposon is expressed in five Jian carp tissues:the liver, kidney, blood, muscle, and gonad, and is slightly higher in the kidney and liver than in the other tissues. Fluorescent in situ hybridization shown that JRE is randomly distributed in Jian carp chromosomes and no regular patterns were found. In conclusion, the complete structure of a retrotransposon found in a previous study was determined. Detailed analyses indicated that it has the typical structure of an LTR retrotransposon. Phylogenetic analysis showed that it is highly similar to JULE transposons. Its copy number in the Jian carp is not high, suggesting that its transcriptional activity is low. These findings extend our knowledge of the structure and features of the Jian carp genome, and might provide a new method of transgenic fish production.