Pomegranate (Punica granatum) is an important horticultural crop of the subtropical regions in the word. In 2016 and 2017, a survey of pomegranate fungal trunk pathogens was conducted in some orchards in Fars and Kerman provinces. Branch samples were collected from affected trees exhibiting yellowing, canker, sparse foliage, dieback and decline. Branch samples were cut lengthways and crossways, and inspected for various wood discoloration. Samples with discoloured internal tissues were cut into small discs (3 × 3 mm) and surface disinfected by immersing in 1.0% solution of NaOCl for 30 second and rinsed in sterile distilled water (SDW). Approximately 12-15 wood pieces were taken from the margin between symptomatic and apparently healthy tissue and plated onto potato dextrose agar (PDA) or malt extract agar (MEA) media. All fungal isolates were identified based on morphological and cultural characteristics. All plates were incubated at 25°C. Morphological identifications of the representative isolates were confirmed by sequence analysis of the internal transcribed spacer (ITS) nrDNA (for Diatrypaceae isolates), partial β-tubulin gene: BT (for Togninaniaceae and Diatrypaceae isolates) and a partial sequence of the translation elongation factor 1α: EF-1α (for Botryosphaeriaceae isolates). In this study, 104 isolates of Togniniaceae (66 isolates of Phaeoacremonium italicum, one isolate of Pm. fraxinopennsylvanicum, five isolates of Pm. inflatipes and 32 isolates of a Phaeoacremonium sp.), 13 isolates of Botryosphaeriaceae (Lasiodiplodia theobromae) and four isolate of Diatrypaceae (Diatrype whitmanensis) were isolated and identified from affected trees. This study is the first record of Pm. fraxinopennsylvanicum, Pm. inflatipes, L. theobromae and D. whitmanensis on pomegranate worldwide. Pm. italicum has not yet been reported from Iran and the present study is the first record of this species for the Iranian mycobiota.