In this report, the amino acid sequence of giant panda interferon-α (gpIFN-α) was determined and compared with 15 corresponding IFN-α sequences. Phylogenetic analysis showed that the 15 interferons fell into two large groups. The giant panda and ferret branched and were most closely related to fox and dog and evolved into a distinct phylogenetic lineage from that of eukaryotic mammalians which evolved into another lineage. After analyzing the encoded amino acid sequence of the gpIFN-α using bioinformatics, the results revealed that in the full amino acid sequence, there were no transmembrane domain, one N-glycosylation sites, eight O-glycosylation sites and nine antigenic determinants. Secondary structure analyzed showed that the Alpha helix, Extended strand, Beta turn and Random coil each occupied 60.37%(99aa), 4.88%(8aa), 9.76%, 25%(41aa) respectively. In conclusion, our results will give the opportunity to investigate more in detail function study in giant panda and add to studies on the evolution of the IFN system in vertebrates and avian more generally.