Cherry leaf roll virus (CLRV) belongs to the genus Nepovirus , in the familly Comoviridae, occurs worldwide. The virus is widespread in North America, Germany, Chile, New Zealand, Australia, China, Hungary, Yugoslavia, Spain, Portugal, Japan and Turkey. Cherry leaf roll virus naturally infects a wide range of woody and herbaceous plants that the most of them belong to the genera Betula , Fagus , Juglans and Prunus . The virus infects elm, blackberry, raerry, walnut, blueberry, stone fruits and other trees and causes severe damage. It has been also detected in many herbaceous plants such as Rheum . Cherry leaf roll virus causes symptoms such as chlorotic spots, leaf curling, enation, dieback, skin cracking, and gum in sour cherry and sweet cherry. In cherry trees, flowering and leaves opening could be delayed. The fruits of infected trees show early blight and swell before maturation. CLRV has been previously reported from olive trees in Zanjan province, but there are no available molecular data for the Iranian isolates of CLRV. During the years 2009 and 2010, for detection and determination of certain molecular properties of CLRV, leaf samples showing CLRV symptoms were collected from stone fruits orchards in Charmahal va bakhtiari and Isfahan provinces. The large number of the collected samples was positive for CLRV in double antibody sandwich-enzyme linked immunosorbent assay (DAS-ELISA) using a commercial polyclonal antiserum against CLRV. The infection of some ELISA positive samples was confirmed by the amplification of a DNA fragment of the expected size (286 bp) in nested-reverse transcription-polymerase chain reaction (nested-RT- PCR) and immunocapture-nested RT-PCR (IC-nested-RT-PCR) with CLRVF/CLRVR primer pair. The amplicons in four isolates including S1 (Zayanderoud border-almond), S2 (Saman -almond), S3 (Natanz-apricot), S15 (Cham-chang-apricot) were cloned and sequenced. The BLAST search revealed high similarity between the Iranian isolates and other CLRV isolates available in GenBank and the amplified segment is a part of 3' non-coding region (NCR) of RNA2. Multiple alignment of the 3'NCR of RNA2 nucleotide sequences of the Iranian isolates and those of other CLRV isolates available in GenBank showed high similarity ranging from 93.5%- 97.5% between Iranian isolates. The highest and lowest similarity were found between Cham-chang-apricot isolate and a German isolate from walnut with accession number AJ877146 (98.2%) and Saman-almond isolate and a German isolate from Sambuscus nigra with accession number AJ877138 (86.9 %.), respectively. Phylogenetic analysis indicated that CLRV isolates were divided into six different phyogenetic groups including A, B, C, E, D1 and D2. The S2 isolate was placed in the phylogenetic group D2 and S15 and S1 isolates were placed in phylogenetic group D1with some