The reproductive biology of three Ziziphus species: Z. jujube, Z. mauritiana and Z. spina-christi, with respect to seasonal growth stages, floral biology, pollen performance, fruit set and seed viability were compared. To elucidate the reasons for variations in reproductive success we also estimated the ploidy levels among the genotypes of these tree species. Four genotypes of Z. mauritiana and Z. jujube each, and two natural selections of Z. spina-christi were grown in the Negev highlands at the Sde Boqer experimental plot. Field observations were conducted to determine seasonal growth stages and floral biology; laboratory studies included florescent microscopy, differential interference contrast microscopy, in vitro pollen germination and histological techniques. Seasonal growth stages were similar in Z. spina-christi and Z. mauritiana but distinct in Z. jujube, which was the earliest species. Flower opening stages were similar in all species and genotypes. Anthesis timing was genotype specific and did not depend on species. Anthesis types were subdivided into early and late morning as well as afternoon. We found a wide range of values for the number of flowers per inflorescence between species and genotypes, but all genotypes set one fruit per inflorescence with the exception of Z. jujube genotype Tamar, which set two fruit per inflorescence. Significant variation in fruit weight was observed between species as well as genotypes. Fruit of Z. mauritiana and Z jujube weighed between 9 to 37 g while fruit weight of Z. spina-christi was between 0.5 to 0.7 g. Flowers of all species and genotypes had two ovules but viable seed set per fruit differed dramatically between species under open pollination. Viable seed set was about 18% for Z. mauritiana and Z jujube, while Z. spina-christi, had the highest viable seed set at about 84%. Histological analysis revealed post fertilization embryo abortion which may be responsible for the relatively low reproductive success in Z. mauritiana and Z. jujube. The results obtained in this study provide an important basis for selecting elite complementary genotypes toward the optimization of Ziziphus fruit production in semi-arid regions.