Sclerotinia stem rot, which is caused by Sclerotinia sclerotiorum, is one of the serious diseases of canola. In a survey during 2016-2017 growing season, Stem rot observed on canola fields in Kohgiluyeh and Boyerahmad province. The first symptom was pale to dark brown lesions on the stem that grew an obvious area of white, fluffy mycelia on the plant infected part. Sclerotia of the fungus formed on the outer surface of the diseased tissue, but sometimes inside of soft host tissues. Eventually, infected plant wilted and died. In order to isolate fungal agent, sampling of various regions were collected. In this study the infected samples from different places with wilting symptoms were collected and transferred to the laboratory. Sclerotia cultured on Potato Dextrose Agar and then incubated in 25°C for one week. After 5-7 days fungal colonies were grown and Sclerotia were plenty produced on PDA. A collection of 29 isolates were purified by hyphal tip method. Species identification was done Based on morphological characteristics (colony, hypha, Sclerotia and other related characters), using valid identification keys. To confirm morphological identification, Single colonies were transferred to flasks containing 50 ml Potato Dextrose Broth and grown on an orbital shaker for 5 to 7 days at 120 rpm at 18°C. DNA extraction was carried out by Murray and Thompson (1980) method. DNA sequence data were generated for the ITS-rDNA region. The pathogen was identified as S. sclerotiorum. This is the first report of isolation and identification S. sclerotiorum from canola fields in Kohgiluyeh and Boyerahmad.