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Genus Ziziphus (Z.) contains various important species in tropical and subtropical regions that are globally famous for their food and medicinal uses. However, no comprehensive study was available on the morphology and phytochemistry of Ziziphus species, mainly under different growth conditions, i.e., irrigated and desert (Cholistan). Therefore, this study was carried out to evaluate the morphological and phytochemical characteristics of Ziziphus species, i.e., Z. jujuba, Z. mauritiana, Z. spina-christi, and Z. nummularia, found in the irrigated and desert conditions. Our results revealed significant variations for most of the measured parameters, showing a large-scale diversity among Ziziphus species under irrigated and desert conditions. Specifically, Ziziphus species showed better morphology of all measured parameters of leaves and fruits under irrigated conditions compared to desert conditions, indicating that the optimum water availability in irrigated conditions improved the morphological parameters of Z. species. Meanwhile, among all Ziziphus species, the maximum leaf length (7.4 cm), leaf width (4.1 cm), leaf area (30.6 cm2), and leaf petiole length (1.3 cm) were observed for Z. jujuba, and the highest leaf dry weight (55.4%) was recorded for Z. mauritiana. Similarly, the highest fruit length (3.9 cm), fruit stalk length (1.5 cm), fruit diameter (3.6 cm), fruit width (3.8 cm), fruit area (66.1 cm2), seed length (2 cm), and seed diameter (1.1 cm) were measured for species Z. jujuba, while the maximum fruit dry weight (49.9%) and seed width (1.4 cm) were recorded for species Z. nummularia. Interestingly, compared to irrigated conditions, higher values of bioactive contents, i.e., phenol, flavonoid, and antioxidant activity, in fruits and leaves of Ziziphus species under desert conditions indicated the positive impact of desert climate on the phytochemistry of the Z. plants. Among Ziziphus species, Z. nummularia accumulated the maximum fruit phenols (304.4 mg GAE/100 g), leaf phenols (314.2 mg GAE/100 g), fruit flavonoids (123.7 mg QE/100 g), and leaf flavonoids (113.4 mg QE/100 g). Overall, this study demonstrated the significant morphological and phytochemical variations of the Ziziphus species under irrigated and desert conditions, which could be utilized for future studies to improve the production and medicinal potential of the Ziziphus, especially in desert areas.