Genetic diversity of 50 bread wheat accessions belonging to 6 botanical varieties was studied using ISSR primers. Only 7 ISSR primers out of 12 which showed a high level of polymorphism were used for the genetic diversity analysis of the studied genotypes. Sixty five polymorphic fragments were identified with these primers and cluster analyses divided all genotypes into 5 main clusters according to the Nei’s similarity index. The results of cluster analysis showed that the genotypes of the same botanical varieties generally were included into one group. This once again confirms the importance of botanical variety traits in breeding. Genetically distinct genotypes can be used in breeding as an initial material. The primers UBC811, UBC-841 and UBC-827 with the highest number of amplified and polymorphic bands, the level of polymorphism and the highest value of genetic diversity, such as PIC, EMR and RP were recommended as the most appropriate primers to study genetic structure of bread wheat genotypes.