Background and Aims: Virus infections represent some of the most important diseases of lily, plants because of the devastating effects caused to the crops and the absence of effective treatments. A survey for virus diseases of lilies, revealed the occurrence of Cucumber mosaic virus (CMV) in plants growing in Tehran province, Iran. Materials and Methods: During 2013, 50 lily samples with virus-like symptoms were collected and tested by ELISA. The presence of the CMV was confirmed by biological assay and RT-PCR tests. Phylogenetic structure, statistical tests of neutrality and genetic differentiation and the gene flow level between populations were evaluated using 2b gene. Results: Thirty seven (74%) out of 50 lily samples were infected with CMV. The host rang of lily isolates was limited to Nicotiana benthamiana, which confirmed by ELISA and RT-PCR. The complete 2b gene nucleotide sequence of lily isolates were 243 nt long. The highest nucleotide identity (99%) was indicated with South Korean LiBC isolate (Ac. no. AB506799). Phylogenetic analysis using 2b gene showed two main groups which, lily isolates were classified into a separate branch in group I. Using the maximum likelihood method, amino acid 55 S in the 2b protein of the CMV isolates in group I was found to be under positive selection. Conclusion: CMV has been previously reported from Iran but, the association of CMV in lily plants represents the first record from Iran. Our information will help to better understand epidemiology and to develop a successful management program for reducing the impact of this disease.