AbstractCrimean‐Congo hemorrhagic fever (CCHF) is a potentially fatal disease caused by a tick‐borne virus in the family Bunyavridae. The disease occurs in parts of Africa, Asia, Middle East, and Eastern Europe. During recent years, an increasing number of human CCHF cases have been diagnosed in Iran, but very little information is available on the prevalence and genetic diversity of CCHFV in Iran. In the present study, CCHF virus (CCHFV) isolates from nine Iranian patients infected during 2002 were examined genetically. Nucleotide sequencing of the S‐ and M‐segments, encoding the nucleocapsid protein (NP) and the glycoproteins, respectively, revealed that the different isolates were related closely to each other with nucleotide sequence identities exceeding 98% for both S‐ and M‐segments. Phylogenetic analysis of partial S‐segment nucleotide sequences showed that the viruses clustered along with strains from Pakistan and Madagascar in one distinct lineage. Phylogenetic analysis also demonstrated that the Iranian isolates examined in this study and the previously published CCHFV strain ArTeh193‐3 clustered into different genetic groups, indicating that at least two genetic lineages of CCHFV could be co‐circulating in Iran. J. Med. Virol. 73:404–411, 2004. © 2004 Wiley‐Liss, Inc.