Apple (Malus domestica), is an important fruit crop that economically is known as a major agricultural product in Iran. Apple is cultivated in many areas of Iran. Many pathogenic fungi have been recorded on apple trees. In this study, in order to identify fungal agents damaging shoot and trunk of apple trees, orchards were surveyed during the years 2016 and 2017 in Western Azerbaijan, Eastern Azerbaijan, Isfahan, Kohgiluyeh and Boyer-Ahmad, Hamedan and Zanjan provinces. Severe damages were observed under environmental stresses such as drought and cold, especially in over 15-year-old orchards. Samples were collected from trees with stem and trunk cankers, shoot dieback, bark necrosis, gummosis and scaling-off of the bark symptoms, and then they were transferred to the laboratory. After surface sterilization of samples, pieces about 1×1 cm were prepared and cultured on potato dextrose agar (PDA). Cultures were incubated at 25 °C for 7 days in darkness. Emerging mycelium was separated and purified using hyphal tip culture on 2% water agar (WA). Morphological characteristics of isolates were evaluated based on fruiting bodies and colony shape and color. The ITS region of representative isolates in some species was amplified and nucleotide sequences were used for BLAST searches with ex-type isolate sequences in GenBank. In the present study, Cytospora rhodophila and C. sorbicola for the first time, C. cincta, C. schulzeri, Diplodia bulgarica, Neoscytalidium dimidiatum, and schizophylum commune were determined as causal agents of apple canker and shoot dieback in Iran. Further studies to identify other agents are in process.