Foo-t and-mouth disease virus strain AF72 RNAs were used as templates for RT-PCR to amplify the target gene.The purified PCR products were cloned into pGEM-T easy Vectors and transformed into E. coli JM109.The positive recombinant plasmids identified by electrophoresis, PCR, and analysis of tow cleavages with Spe I and Sph I. The nucleot ide sequence were confirmed by comparing with the ful-l length sequence of the other reference strains. By homology modeling, the 3D model of AF72 VP2 structure protein was obtained.Then several parameters, including hydrophilicity, flexibility, antigenic index and surface probability were integrated, and B-cell epitopes in VP2 were predicted. After analyzing the difference among VP1, VP2, VP3, VP4, at the nucleotide level, the mutation rates of these 4 encoding sequences were no difference ( P > 0105), however, at the amino acid level, those mutation rates were different ( P< 0105).The regions of 1- 23th, 37- 51th, 66- 76th, 85- 101th, 124- 142th, 165- 199th, 205- 219th in VP2 protein most probably are conservative. This research should be used as an instruction in order to direct the work on FMDV VP2 protein, and Bcell epitopes in VP2 probably exist in the following regions: 1- 10aa, 129- 140aa, 165- 176aa. This result offers valuable information for research of FMDV mult-i epitope vaccine.