Orobanche cumana is an obligate root parasite of sunflower. It represents a major agricultural problem in many countries of southern and eastern Europe. Information on O. cumana population genetics, structure and dynamics is scarce, particularly due to the lack of suitable molecular markers for such studies. The objective of this study was to identify and characterise simple sequence repeat (SSR) markers for O. cumana. Four thousand two hundred SSR-containing candidate sequences were obtained from O. cumana using next-generation sequencing, from which 298 SSR primer pairs were designed and 217 of them used for validation. Seventy nine SSR primers produced reproducible, high quality amplicons of the expected size that were polymorphic among 18 O. cumana populations from different geographical locations and hosts (sunflower, wild hosts from the Compositae family). The number of alleles per locus ranged from 2 to 10, with an average polymorphism information content value of 0.37. The O. cumana SSR markers were highly transferable to the closely related species Orobanche cernua. SSR markers showed high resolving power; UPGMA cluster analysis allowed proper classification of Orobanche spp. samples into species (O. cumana and O. cernua), geographical origin and host. The functional SSR markers reported in this study constitute a valuable tool for genetic analyses in O. cumana and related species and will contribute insights into the biology and genetics of this parasitic weed.