In recent years, it has been reported the increasing harmfulness of Dia- porthe/Phomopsis spp. in the orchards and nurseries worldwide. They cause nonspecific symptoms which in combination with the morphological similarity of the cultures and difficult sporulation creates problems with their correct identification using classical methods. This implies the need to integrate advanced molecular techniques to identify the strain on the species level. The aim of this research was to determine the identity and genetically characterize forty isolates of Diaporthe/Phomopsis obtained in 2010–2012 from the shoots of selected fruit trees grown in the south-eastern Poland. Using the RAPD-PCR technique the genetic similarity within studied population has been demonstrated irrespectively of the origin and type of the host plant from which the isolates derived. Based on the comparative analysis of the non-coding sequence of the ITS regions (ITS1, 5.8S rDNA, ITS2) with the sequences available in NCBI database the studied Diaporthe isolates were identified as Diaporthe eres species complex not described previously on fruit trees under Polish conditions.

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