We collected serum samples from the randomly selected “dancing pigs” from a large-scale pig farm in Hunan Province, and identified them by RT-PCR using primers for the NS5B and E2 genes that can amplify the atypical porcine pestivirus(APPV), and then sequenced the PCR amplified products. Subsequently, the homology of NS5B and E2 gene sequences was analyzed using MegAlign software to predict part of the structure of the E2 protein, and the genetic evolution tree of NS5B and E2 genes was constructed using the neighbor-joining method, using MEGA 5.0. It indicated that the affected piglets were positive for the atypical porcine pestivirus(APPV) infection. The homology of the gene sequences of strain HN0626 with those of 84 reference strains of NS5B and E2 in GenBank was identified as 81.68%- 98.95% and 81.14%-99.33%, respectively, and its potential B-cell antigenic epitopes were successfully deduced. Phylogenetic analysis showed that strain HN0626 belongs to genotype 1, which is the main prevalent strain in the global swine population, and its E2 and NS5B gene sequences were accessed in GenBank with the accession numbers OR936135 and OR936136, respectively.