The xerophytic shrub Ziziphus lotus (L) Lam may constitute the best choice as a fruit crop in arid regions and seems to have a great importance in uncultured and marginal soils. As the first report, this study investigates the genetic diversity among and within nine natural populations of Z. lotus encompassing wide range of ecological conditions in Algeria through analyses of fruits characteristics. Results reveal significant differences of fruit traits among and within populations; the morphological variability was significantly correlated with the variation of ecological conditions. In general, fruits color ranges from light to dark brown with mostly oval-shaped endocarps containing one or two seeds. In addition, fruits weight ranged between 0.43 and 0.75g while length was comprised between 10 and 13mm and fruit thickness varied between 9.85 and 12.81mm. Overall, quantitative traits were significantly influenced by the environmental conditions, whereas qualitative traits were not clearly affected. Hence, three phenotypes were distinguished allowing detection of a gradual phenotypic variation following latitudinal gradient related mainly to aridity and sand content in the soil. Such variation offers a good basis for breeding objectives, principally for food and medicine objectives along with wide adaptations for various range of climate and soil. Management and conservation of Z. lotus germplasm in Algeria is highly recommended.