Deformed wing virus is one of the most common viral infections in honeybee populations around the world. In this study, a total of 30 apiaries located in different geographical regions of Hamedan, Iran were analyzed for the presence of deformed wing virus on capped larvae and workers of the honeybee, Apis mellifera (Hym: Apidae), as well as the parasitic mite, Varroa destructor (Acari: Varroidae), using reverse-transcription PCR. Two target sequences within the putative VP1, VP4, and VP2 structural-protein genes and the RNA helicase enzyme gene, were selected for amplification and sequencing. According to the results, 36.6% of apiaries were found to be infected with deformed wing virus, including 8, 0, and 3 positive samples on capped larvae and workers, and Varroa mites, respectively. Four strains of the virus obtained from honeybees and mites were selected for analysis of genetic diversity and phylogenetic relationships with other sequences deposited in GenBank. The results showed a high degree of similarity between the virus strains in honeybee and Varroa mite. The phylogenetic results highlight the higher suitability of non-structural in comparison with structural proteins for genetic diversity and phylogenetic studies of deformed wing virus strains.