The present study was conducted on five ber (Ziziphus mauritiana Lamk) cultivars (Komethry, Pakstany, Um-sulaem, Toffahy and Peyuan) grown in Saudi Arabia during 2005 and 2006 seasons. The aim of the present study was to investigate fruit properties (fruit weight, length, diameter, shape, specific gravity, seed weight, pulp percentage, total soluble solids (TSS), acidity percentage, TSS/acid, vitamin C content total, reducing and non-reducing sugars). Peyuan cv. had the heaviest fruit weight, fruit volume and reducing sugar content however, it was the lowest in pulp percentage and non-reducing sugars among the five cultivars in both seasons. Toffahy cv. had highest fruit diameter and seed weight while, had lowest TSS %, vitamin C and total sugars values. Um-sulaem cv. had highest acidity percentage and vitamin C content and lowest fruit weight, length and TSS/acid. On the other hand, Pakstany cv. had highest percentage of both pulp percentage, TSS, total and non-reducing sugars. Finally, Komethry had the longest fruit. The molecular characterization and fingerprint identification of the ber cultivars was conducted using the ISSR (Inter-Simple Sequence Repeats) technique. The ISSR technique was able to uniquely characterize and differentiate between the five ber genotypes. Moreover, the genetic similarity tree showed that the cultivar Um-slaem is genetically distant from the other four cultivars and the two cultivars Pakstany and Komethry were genetically identical.