The complete genome of Iranian isolate of Bean leaf roll virus (BLRV-Iran) was sequenced using an infected faba bean plant from Zafarabad region in Shiraz. In order to complete the full-length genome sequence of the BLRV-Iran, primers from the different region of the genome of the Iranian and American isolates of the virus, with the Accession numbers MF780970 and AF441393, respectively, were designed and used in RT-PCR and sequencing reactions. Then, the full-length genome of BLRV-Iran was amplified and cloned in a pTZ vector. The complete genome of BLRV-Iran was determined to be 5904 nucleotides (nts). Comparson of the the complete nt sequence of BLRV-Iran with those of American isolates (HM439776 and AF441393) and Argentina isolate (KR261610) of BLRV available in GenBank was indicated that a 19 nucleotides region was absent in the non-coding region (UTR) of the 3′ end of the BLRV-Iran genome. The lack of this region in BLRV-Iran genome was confirmed after cloning of the virus genome in pTZ. The existence of this region in the UTR region of the 3′ end of the American and Argentine BLRV isolates genomes and its lack in the same region in the BLRV-Iran genome indicated a major difference in the genome of BLRV in different geographical regions of the world. Comparison of obtained nucleotide (nt) sequence of complete genome of BLRV-Iran with corresponding nt sequences of other BLRV isolates available in the GenBank indicated that BLRV-Iran had the highest (94%) and the lowest (93%) similarity with Argentina isolate and American isolate (Hm439776) of BLRV, respectively. Finally, phylogenetic analysis of nt sequences of the complete genome of the BLRV isolates revealed two clusters. One cluster is composed of BLRV-Iran and the other cluster included the American and Argentina isolates. It is noteworthy that in the American and Argentine isolates cluster, one of American isolates with Accession number of HM439776 showed more proximity to Argentina isolate compare to another American isolate with the Accession number of AF441393.