DNA based molecular markers allow precise, objective and rapid cultivar identification and discrimination. In the present study, the genetic variability and relationships among 65 hexaploid (Triticum aestivum L.) and 8 tetraploid (Triticum durum L.) wheat varieties were evaluated using five inter simple sequence repeats (ISSR) primers. The used primers generated 63 DNA fragments with an average of 12.6 bands per primer. Polymorphism percentage ranged from 53.33 % (ISSR-844) to 78.57 % (HB12) with an average of 64.95 %. The 308bp (HB12) DNA fragment was unique marker for durum wheat varieties while the 855bp (ISSR-814) fragment was unique maker for bread wheat genotypes. Low PIC values were found indicating the wide differences between the p and q alleles tested by the ISSR markers. The ISSR primers (HB12 and ISSR-844) possessed high RP values and therefore seem to be the most informative primers for distinguishing wheat varieties. The dendrogram indicated that the ISSR markers succeeded in distinguishing the tested varieties in relation to their ploidy level and location, which the tetraploid varieties were put together in one group as well as the hexaploid varieties.