Sacbrood virus (SBV) is one of the most common and harmful viruses to honeybees. It causes failure to pupate and death during larval stage, in adult bees it has an influence on their behavior and even shortens their life-span. In this study, we analyzed the phylogenetic relationships among the SBV isolates from all around the world, with from both Apis cerana and Apis mellifera. Phylogenetic trees were constructed based on three types of nucleotide sequences: complete genome sequence, VP1 gene and SB1-2 fragment of SBV. Moreover, genome recombination analysis was performed to assess the effect of genome recombination on the evolutionary relationship of some SBV isolates. The phylogenetic trees showed that although all the SBV isolates form two major groups, these two groups were not formed strictly according to their host specificity or geographical origin. These results indicate that both host specificity and geographic origin decide the genetic diversity of SBV strains.