Abstract: A pair of cloning primers were designed according to the cloning principle of in silico sequence. The whole coding region of interferon epsilon1(IFNE1) extracted from mucosal tissue of porcine stomach was amplified by RT-PCR, and sequence analyzed. Then, a pair of expression primers were designed according to the cloned sequence. A fragment of porcine IFNE1 cDNA containing EcoRI/XhoI were amplified from recombinant vector by PCR. The fragment was to construct a recombinant expression vector. Subsequently, the recombinant vector were transformed into parasitic bacterium. The fusion protein, which was induced was confirmed by SDS-PAGE.The results showed that the cloned sequence contain the open reading frame of 582 bp and encodes 193 amino acids. Identity analysis showed that the porcine IFNE1 nucleotide sequence shared 83.6% and 69.2% homology with that of human, mouse, the predicted amino acid shared 76.2% and 55.2% homology with that of human, mouse. The fusion protein expressed in E.coli BL21(DE3) was about 47 kDa and mainly existed as inclusion bodies.