The purpose of the study was to determine which fungal species colonize the shoots of apple, pear, cherry, plum, apricot and peach in south-eastern Poland and whether Diaporthe (Phomopsis) isolates there are among them. The study was conducted in 2010–2012 and the plant material was collected from five orchards. In three of these chemical controls were carried out, while there was no protection applied in the other two. The results showed that species composition of the fungi was very similar regardless of host plant and year of study. Alternaria spp., Fusarium spp. and Phoma spp. were isolated most frequently from the studied shoots. Fungi cultures known for pathogenicity towards fruit trees such as Botrytis cinerea, Colletotrichum gloeosporioides, Leucostoma spp., Monilinia spp. and Neofabraea spp. were also isolated. Moreover, there were isolates of Diaporthe (Phomopsis) among the fungi present in the shoots. Cultures of these fungi were obtained both from shoots with disease symptoms and from visually healthy ones but mainly from shoots originating from unprotected orchards, what indicates their greater threat to fruit trees grown without chemical protection. This is the first documented report of the occurrence of Diaporthe (Phomopsis) on fruit trees in Polish conditions.