Beet black scorch virus (BBSV) a species of the Betanecrovirus genus, in the family Tombusviridae are among the drastic and considerable threat to sugar beet (Beta vulgaris) field crops worldwide. In recent years, the infection of BBSV has been reported form some Iranian sugar beet cultivation areas. This virus induces severe, systemic disease symptoms by black scorching leaves tips, necrotic fibrous roots and severe stunting of affected sugar beet plants. Although in some case it did not induce black scorching on the leaves but showed exacerbated symptoms like of rhizomania, which induced by Beet necrotic yellow vein virus-BNYVV. The isolates used in this study were isolated from soil samples collected from various sugar beet fields in North-West and North-East Iran provinces and were assayed for virus reaction in greenhouse tests. Soil samples used consisted of autoclaved sand and BBSV-infested soil. Soil samples were mixed in equal parts with autoclaved sand to facilitate ease of root removal of susceptible cultivar Jolge plants at harvest. After six weeks, total nucleic acids were extracted using Tri-reagent from root sugar beet samples and the 3’UTR region were amplified using specific primes and sequenced. The sequences of BBSV isolates were compared to process a comprehensive overview of the genetic diversity in BBSV. Phylogenetic analyses using Neighbor Joining (NJ) implemented in MEGA5, partitions most of the BBSV sequences into two major groups. The Iranian subpopulation in North-West has become more diverged recently. Genetic recombination is critical in the formation of new virus strains. Furthermore, it also strongly shapes the genomes of plant RNA viruses. It seems that intra-recombination in 3’UTR has critical role in emergence of this sub-population. This information is important in breeding programs for sugar beet cultivars resistant to sugar beet soil-borne viruses including BBSV.