Ziziphus spinia-christi and Z. mauritiana are known as "Balady" and "Hendi" cultivars, respectively in Egypt. They were used in this study to analyze the genetic diversity of Egyptian Ziziphus and to authenticate a new superior cultivar namely "Hozaien". This cultivar arose more than fifty years ago and has been reported as a bud sport mutation of "Balady" cultivar despite its extremely morphological and biochemical variations. The sequence related amplified polymorphism (SRAP) and the randomly amplified polymorphic DNA (RAPD) molecular markers were utilized to analyze the genetic relationships amongst the three cultivars. A total of 141 SRAP and 75 RAPD amplicons were generated by 10 SRAP and 6 RAPD primer combinations; of which 87 (61.70%) and 32 (42.67%) bands were polymorphic, respectively. SRAP was more informative and showed more shared and specific unique bands than RAPD. Both cluster analysis and principal coordinate analysis based on SRAP and RAPD data clearly showed that "Hozaien" cultivar has low genetic relationship with Z. spina-christi and should not be classified as a mutant of it. This result encourage us to detach this cultivar from which and subject it for more study, using more species from neighbor countries, to voucher its identity either a cultivar of another species or a new species.