Endophytic fungi are known components of plants biodiversity and infer numerous beneficial effects to host plants. These fungi are cosmopolite, have high biodiversity and live in internal tissues of living plants without any symptoms. The aim of this study was to identify the endophytic fungi of Pterocarya fraxifolia tree. Sampling from healthy branches of Pterocarya fraxifolia trees was done. 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. All of fungi was consistently identified on the basis of morphological characteristics. In order to molecular identification the DNA extraction was done by the CTAB containing buffer. The internal transcribed spacer (ITS) regions of ribosomal DNA was amplified using ITS4 and ITS5 primer pairs. After sequencing of PCR products, the obtained sequences were compared with the related sequences presenting in GenBank. The BLAST and bioinformatics analysis showed 99 % similarity with Neosetophoma samarorum, Xylaria heliscus, Paraphaeosphaeria neglecta and 100 % similarity with Cladosporium perangustum, Microascus murinus. The molecular characteristics of the studied fungi were confirmed by morphological characteristics. Among the identified fungi Paraphaeosphaeria neglecta, Microascus murinus, Neosetophoma samarorum are as new taxa for mycoflora of Iran. Besides, all identified species are new endophytic records from Pterocarya fraxifolia trees.