Broomrape (Orobanche cumana) is one of the most important parasitic plants that drastically reduces sunflower yield. The majority of existing resistance varieties have become insufficient for crop protection. Breeding for broomrape resistance is regarded as the most effective and environmentally friendly control measure. In this paper, mapping of a resistance gene for broomrape races E was performed in a recombinant inbred line population by bulk segregate analyses (BSA) combined with genotyping by-sequencing technology. One QTL with resistance candidate genes was mapped on 5 ​kb interval location from 157,393,001 to 157,850,000 on chromosome 3, the other QTL was located at 5,000 bp interval location from 173,910,001 to 173,915,000 on chromosome 14. Genomic region on candidate interval of chromosome 3 revealed 6 genes with potential resistance for broomrape including transcription factor MYB1R1, Phylloplanin, histone-lysine N-methyltransferase, methylglutaconyl-CoA hydratase, fasciclin-like arabinogalactan protein and fatty acid dehydrogenase. Two resistant genes on candidate interval of chromosome 14 were discovered with potential resistance for broomrape, which were ABC transporter C family member and Ethylene-responsive transcription factor. These precise locations would be valuable for selecting resistant genotypes in future.