Background and Aims: Citrus exocortis disease is naturally limited to citrus plants and causes a serious disease on sensitive rootstocks such as trifoliate orange. The aim of this study was to sample new variants of citrus exocortis viroid from Fars trees with yellowing and suberization symptoms and comparison with other isolates of this viroid.

Materials and Methods: A number of symptomatic or symptomless citrus trees were sampled and studied for viroid detection. After RNA extraction, reverse transcription-polymerase chain reaction was conducted and the full length genome of viroids were cloned and sequenced. Three CEVd isolates from Fars were selected and used for comparison with four CEVd isolates from Mazandaran and a number of other sequences from GenBank.

Results: It was shown that on the basis of homology, three CEVd isolates from Mazandaran and all three CEVd isolates from Fars clustered into one group while one of the Mazandaran sequences fell apart.

Conclusions: Therefore we proposed that Iranian CEVd isolates except one isolate from north have the same origin.