Molecular characterization of Cucumber mosaic virus (CMV) was done by using samples from tomato and cucurbitaceous plants collected from different locations in the northwest region of Iran. After screening by enzyme-linked immunosorbent assay, 91 CMV-infected samples were identified. Biological properties of eight representative isolates were compared with each other revealing two distinct phenotypes on squash and tomato plants. Phylogenetic analyses based on nucleotide sequences of the coat protein (CP), movement protein (MP) and 2b of the new isolates, together with that of previously reported isolates, led to the placement of the Iranian isolates in subgroups IA and IB according to CP and MP genes, but in subgroup IA according to the 2b gene. These data suggest that reassortment may have been a major event in the evolution of CMV in Iran, and that the Iranian isolates are derived from a common recent ancestor that had passed through a bottleneck event.