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Sunflower (Helianthus annuus L.) is an important crop that its oil has nutritional and high economic value. Basal stem rot, caused by Sclerotinia sclerotiorum and S. minor, is one of the important and devastating disease of sunflower. The use of resistant cultivars is considered as the most important and effective method to control the disease. In this study, the reaction of 100 oily sunflower lines to three isolates of S. sclerotiorum and three isolates of S. minor was studied. Identification of gene loci associated with resistance to disease was done with markers produced with 30 SSR primers pairs. The results showed that some of sunflower genotypes had well resistant to Sclerotinia disease. Population structure analysis using Structure software identified 2 subpopulations (K=2). Association analysis using TASEEL software with general and mixed linear models (GLM and MLM) identified 14 and 12 loci, respectively that have significant association with resistant genes related to Sclerotinia. ORS617 locus was commonly related to genes associated with resistance to M1 from S. minor and J1 from S. sclerotiorum. The common markers are important in sunflower breeding programs making possible simultaneously selection for several traits and producing resistant cultivars to Sclerotinia disease.