Walnut anthracnose is the most important fungal disease in Persian walnut in Iran and all over the world caused by Ophiognomonia leptostyla. Limited attempts to genetic variation uncovering in this species were not successful by now. In this study, genetic diversity of 75 Ophiognomonia leptostyla isolates collected from the northwest of Iran was studied by RAPD and ISSR primers. RAPDs revealed more polymorphism in studied isolates than ISSRs, but fewer bands were produced. There were slight correlations with obtained RAPD dendrograms with homothallism and collection site, but no correlation with phenotypic traits in ISSRs. Population analysis identified genetic relationship between neighbor provinces but isolates from Tehran and West Azarbaijan with reasonable distance were relative according to trees were obtained by RAPD and ISSR fingerprinting. Using both markers were useful in genetic variation understanding of the species unlike ITS and LSU RFLP techniques were used in previous researches.