Abstract BACKGROUND Cultivated tomatoes are highly susceptible to the destructive parasite Phelipanche aegyptiaca . Wild relatives show the potential resistance for genetic improvement. However, their genetic and molecular mechanisms are still unknown. RESULTS Among 50 wild tomato accessions were evaluated for resistance to P. aegyptiaca , most of the wild relatives exhibited varying degrees of resistance compared to the cultivars. Solanum pennellii LA0716 performed the most promising and solid resistance with very low infection by the broomrape. The resistance involved in LA0716 was further confirmed by cytological analysis, and explored by employing a permanent introgression line (IL) population. Thirteen putative quantitative trait loci (QTLs) conferring the different resistance traits were identified. They are located on chromosomes 1, 2, 3, 4, 6, 8 and 9. The most attractive QTLs are positioned in IL6‐2 and overlap with IL6‐3. Specially, IL6‐2 showed the highest and most consistent resistance for multiple traits and explained the major phenotypic variation of LA0716. Analysis of candidate genes involved in these regions showed that Beta ( Solyc06g074240 ) and P450 ( Solyc06g073570 , Solyc06g074180 and Solyc06g074420 ) genes are substantially related to the strigolactone (SL) pathway. Transcript analysis further demonstrated that both Solyc06g073570 and Solyc06g074180 might play an important role in the reduction of P. aegyptiaca infection. CONCLUSION Germplasms resistant to P. aegyptiaca were found in wild tomato species. QTLs conferring P. aegyptiaca tolerance in LA0716 were identified. IL6‐2 is identified as a prospective line possessing the major QTLs. The candidate genes would provide the availability to assist the introgression of the resistance in future breeding programmes. © 2020 Society of Chemical Industry