Apple as one of the most important and economical pome fruit plants in west Azarbaijan province, is attacked by different plant pathogens which reduces plant growth and productivity and finally causes severe economic losses to growers. A general inspection of apple orchards in different locations of west Azarbaijan province revealed the high incidence and wide distribution of trunk and branch diseases in these plants. In the present study which is done to determine the fungal pathogens related to apple trunk and branches, numerous samples with suspected symptoms to Cytospora canker disease were collected. The collected samples were first washed thoroughly under tap water, then were surface sterilized using 3% sodium hypochlorite solution for five minutes and again washed with sterile distilled water. Isolation of the fungi were done by growing the infected samples on PCA and PDA culture media. Purification of the isolated fungi were done using single spore method. Based on combination of morphological characteristics and sequences obtained from multiple genomic regions (ITS, RPB2, Actin and LSU), Cytospora paratranslucens was identified. Pathogenicity of the isolates were evaluated on excised apple branches, Golden Delicious and Red Delicious cultivars in In Vitro conditions. Results showed that all the isolates were pathogenic on both cultivars and showed symptoms of bark and wood browning and dying, although virulence of the isolates was greater in Red Delicious cultivar than the Golden Delicious. Re-isolation of the inoculated fungi from the infected branches confirmed the Koch’s postulates. This is the first report indicating the presence and pathogenicity of Cytospora paratranslucens from apple trees in Iran.