Deformed wing virus(DWV) is one of infectious disease of honey bee that is caused to wings of immature or mutation and death at last. In this study 4 kinds of polyprotein of DWV are compared and then selected 2 kinds of polyprotein, RNA-dependent RNA polymerase(RdRP) and peptidase C3G, which has relatively higher homology than others. Analysis of both RdRP region and peptidase C3G of DWV deposited in Genbank of NCBI showed 99~100% and 95~97% of homology on genomic level, respectively whereas analysis of CRPV-capsid and RNA helicase showed 86~98% and 89~98% of homology, repectively. According to the result of gene analysis, two kinds of polyprotein are constructed and analyzed the homology, resulting in RdRP and Peptidase -C3G showed about 96% and 97% of homology, respectively. It indicated that both region is able to use for generation of specific antibody for the diagnosis of Deformed Wing Virus (DWV).