In this study and in order to examine the biodiversity of endophytic fungi from pepper plants in west Azarbaijan province, healthy plants were collected from different growing locations in the studied area. Isolation of the fungi were done immediately after transferring the collected samples to the laboratory. Firstly, plant samples were washed thoroughly under tap water to remove surface microorganisms. Then, surface disinfection were done by dipping the samples respectively in 75% ethanol for one minute, 3% hypochlorite sodium for 2 min, 75% ethanol for 30 sec and finally were washed three times in sterile distilled water. Small pieces were cut separately from each of disinfected plant parts: root, stem and leaf and were placed in Petri plates containing potato dextrose agar (PDA) and potato carrot agar (PCA) media amended with 100 ppm of streptomycin sulfate and penicillin G antibiotics. Fungi growing out of plant samples were isolated and purified based on hyphal tip or single spore method. At all, 18 isolates with typical morphological characteristics of the genus Rhizoctonia were obtained. Nuclear staining were done with safranin O staining solution and isolates were grouped as multinucleate and/or binucleate Rhizoctonia. Anastomosis reaction was studied among the isolates and they were grouped in three anastomosis groups. In each group, an isolate was selected and ITS rDNA region was amplified and sequenced. Rhizoctonia solani AG-4, and anastomosis groups A and G from binucleate Rhizoctonia were identified. This is the first report of Rhizoctonia anastomosis groups as endophytic fungi from pepper plants in Iran.