Ziziphus jujuba var. spinosa ( Z. jujuba ), an important medicinal and edible plant, is well-known for its sedative properties. However, the factors influencing spatial variation in Z. jujuba quality, as well as the relative contributions of environmental and genetic factors, remain poorly understood. In this study, the eastern foothills of the Taihang Mountains were selected as the study area. By integrating phenotypic and chemical analyses, SCoT molecular markers, and mixed-effect modeling, we