Acquiring sufficient information on genetic variation, genetic differentiation, and the ecological and genetic relationships among individuals and populations is essential for establishing guidelines on conservation and utilization of the genetic resources. The aim of this work was to assess the extent and pattern of genetic variation in date palm cultivars: genetic diversity and structure of populations occurring over a wide geographical range and variation in drought adaptive traits. The investigated cultivars and populations originated from Sudan and Morocco. Complex genetic relationships were detected among the plants, and that suggests the role of the tree’s biological nature, isolation by distance and environmental effects on structuring date palm gene pool, and a great human impact. Also, compositional and morphological traits were strongly differentiated among cultivars and phenotypes, as soft and dry date phenotypes showed significant genetic divergence and responded differently to water stress. This work provides new and important results, both for science and practical purposes, and gives new ideas for how to proceed in research on date palm.