To investigate the kinship between the Inner Mongolia pandemic strain and representative strains of the Jaagsiekte sheep retrovirus (JSRV), total DNA from the lung tissue of a JSRV-infected sheep in Inner Mongolia was used to clone fragments of gag, pro and pol genes. The recombinant plasmid pMD-JSRV (including complete genomic sequence of the JSRV strain isolated from Inner Mongolia) was constructed by linking all the cloned fragments with long terminal repeat (LTR) and env gene fragments (cloned previous and reserved by our research team). Sequence analyses revealed that the genome was 7690 bp in length and contained several typical molecular markers for exogenous form of JSRV. These included the Sca I restriction site in the gag gene, two predicted "CCHC" motifs of zinc finger in the encoded nucleocapsid protein and the predicted "YXXM" motif in the TM region of Env. Homology analyses showed that the virus strain belonged to the JSRV type II. pMD-JSRV and AF105220 strains shared a nucleotide identification of 95%. The full length genomic clone of JSRV could provide a molecular basis for an infectious JSRV molecular clone as well as an experimental platform to study the detection and pathogenesis of JSRV.