Alternaria is a ubiquitous fungal genus that includes saprobic, endophytic and pathogenic species. Fungal endophytes are group of fungi that internally infect living plant tissues whithout causing any visible manifestation of disease. In order to identify the endophytic fungi from Crataegus pentagyna trees, during the 2015-2016 years, samples were taken from brauches of healthy Crataegus pentagyna trees of Talesh. For initial disinfection, samples were primarily washed with tap water and After separation of bark from wood, wood fragments were cut into small pieces of .5 cm. Samples were surface sterilized whit 75% ethanol(v/v) for 1 min, 2% sodium hypochlorite (v/v) for 3 min and 75% ethanol(v/v) for 1 min respectively, and then washed three times whit autoclaved water, and then drying in a sterile filter paper samples were plated onto PDA culture medium and incubated at 25°C for 4 weekes. The samples were purified by single spore and hyphal tip methods after growth. All of fungi was consistently identified on the basis of morphological characteristics. Among the samples, the fungi of the genus Alternaria were identified based on morphological features of Conidium, Conidiophore and Sporulation pattern of specimens were identified on the PCA medium. In order to molecular identification the Internal Transcribed Spacer (ITS) regions of ribosomal DNA was amplified using ITS4 and ITS5 primer pairs.Morphological identifications of these isolates were confirmed by sequense analysis. This is the first report of A.infectoria, A.citri, A.burnsii, A.alternata on Crataegus pentagyna trees from Iran. Also, all identified endophytic fungi are reported from Crataegus pentagyna for the first time.