Forty‐eight fig orchards were surveyed to determine the presence and incidence of Fig cryptic virus (FCV), Fig fleck‐associated virus (FFkaV), Fig leaf mottle‐associated virus 1 (FLMaV‐1), Fig leaf mottle‐associated virus 2 (FLMaV‐2) and Fig mosaic virus (FMV) in four provinces of northeast, northwest and central regions of Iran. A total of 197 leaf samples from commercial and outdoor fig gardens were collected in April and September 2012 and tested by reverse‐transcription polymerase chain reaction (RT‐PCR). Approximately 14.7% of the tested fig trees were infected by FCV, FFkaV and FMV with a peak of 18% in Tehran province. None of samples was found to be infected with FLMaV‐1 or FLMaV‐2. FFkaV was found in fig trees collected in all the four provinces, but no FCV infection was found in Semnan province, and FMV was just occurred in Markai and Tehran. Mixed infections of FCV with FFkaV and FMV were detected in 2.5% of the samples. The sequence of the CP fragment of six Iranian FCV isolates showed 97–99% nucleotide (nt) identity with the reference FCV isolate, while that of a RdRp and Gp fragments of nine FFkaV and two FMV Iranian isolates showed 87–91% nt and 89–90% identity with the reference isolates, respectively. Phylogenetic analysis grouped the FCV and FFkaV isolates in two distinct clusters, with the Iranian isolates included in both clusters. Results showed genetic diversity among Iranian viruses. Structure and diversity of FCV and FFkaV populations are discussed.
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