Microsatellite loci represent prevalent molecular markers for assessing genetic diversity, phylogenetic and evolutionary relationships between different in origin broomrape taxon. In the present study, the genetic differences and relationships among 3 broomrape races from Bulgaria, Turkiye, Moldova and Romania were identified by ISSR markers. The obtained results on genetic diversity parameters showed that race H is more variable than races G and E. However, the gene diversity within populations was the greatest in race G, followed by race H and E. The limited gene flow for races H and G determined significant genetic differentiation of populations. Conversely, a comparatively moderate gene flow for race E pointed to a little differentiation among populations. These findings were also corroborated by AMOVA, demonstrating high genetic diferences within (89%) and lower (11%) among races. The investigation also revealed the existence evolutionary differences between all races. This situation proves the action of evolutive molecular mechanisms which offered, in time, discrete genetic particularities at broomrape, indicating that the existing races are unstable over time and they are constantly adapting to the new more sunflower resistance hybrids.