genetic variation and identification of taxons with high levels of accuracy and reproducibility. Among the many types of molecular markers, ISSR can be useful for studying genetic diversity and phylogenetic relationships, DNA fingerprinting in the identification of closely related taxons, and also for genome mapping. The main purpose of our study was to investigate the effectiveness and acceptability of ISSR marker system use to analyze the genetic diversity, explore genetic kinships and discriminate among 23 Orobanche cumana populations belonging to 3 races (E, H and G) collected in the territory of 4 countries from the Black Sea basin (Bulgaria, Romania, Moldova and Turkey). Molecular profiles obtained for 23 populations based on 13 ISSR-markers has allowed revealing both the significant differences and similarities depending on the analyzed population or type of primer. As a result of the ISSR markers usefulness assessment for determining of broomrape population genetic diversity by means of the statistical indices (number of total loci from 4 to 36, percentage of polymorphism from 70 to 100%, PIC from 0.052 to 0.281, hj from 0.001 to 0.480, Rp from 3.583 to 17.333, MI from 0.120 to 8.280, EMR from 2.250 to 30.250), three dinucleotide ((AG)8YA, BC857, BC841) and one trinucleotide ((CAG)5) primers were identified as the most informative. ISSR analysis of the different race broomrape populations revealed quite high levels of DNA polymorphism (races E–87%, G–91% and H–94%). However, it should be noted that the specific loci were detected in all races: race E–11.63% or 15 loci out of 129, race G–8.88% or 23 loci out of 259, race H–5.44% or 16 loci out of 294. But as for the common loci, they were observed only in the race E. Thus, this analysis detected that the race E contains the highest percentage of specific loci which possible evolutionarily distances her from the race G and H, as can be seen from our findings. Additionally, the frequency distribution allele analysis just confirms once again the conclusions that races G and H are more similar to each other, which means, that race E is more distant of races G and H in evolutionary time. And furthermore, the genome of race E is more stable than at the races G and H.