Fungi are associated with the European cranberry (Vaccinium oxycoccosL.) and play important roles in plant growth and disease control, especially in cranberry yields. This article presents the results of a study which was aimed to investigate the diversity of fungi found on different clones and cultivars of the European cranberry grown in Lithuania, causing twigs, leaf diseases and fruit rots. In this study seventeen clones and five cultivars ofV. oxycoccoswere selected for investigation. Fungi were isolated via the incubation of twigs, leaves and fruit on a PDA medium and identified according to their cultural and morphological characteristics. Microscopic fungi belonging to 14 genera were isolated from cranberry leaves and twigs, withPhysalospora vaccinii,Fusariumspp.,Mycosphaerella nigromaculansandMonilinia oxycoccibeing the most frequently isolated fungi. ‘Vaiva’ and ‘Žuvinta’ cultivars were the most susceptible to pathogenic fungi during the growing season. Among the clones, 95–A–07 was the most susceptible toPhys. vaccinii, 95–A–08 toM. nigromaculans, 99–Ž–05 toFusariumspp. and 95–A–03 toM. oxycocci. Microscopic fungi belonging to 12 genera were isolated from cranberry berries. The most prevalent pathogenic fungiM. oxycocciwere isolated from the berries of the cultivars ‘Vaiva’ and ‘Žuvinta’ and clones 95–A–03 and 96–K–05.