Morphological and molecular analyses were conducted to evaluate the genetic diversity among eleven Egyptian date palms (Phoenix dactylifera L.). Ten SSR primer pairs revealed a high percentage of polymorphism (97.4%) among 38 total number of alleles, while 11 SCoT primers produced 48.5% from 171 amplified fragments. SCoTs recorded effective multiplex ratio (EMR) and PIC values of 7.5 and 0.14, respectively, opposing to 3.7 and 0.26 for SSRs, respectively. A similar marker index has thus resulted in both markers. Nei's gene diversity (h) was generally low for both marker systems indicating homogeneous nature and narrow genetic background for the studied Egyptian date palms, which was also emphasized through their high genetic similarity estimates. The results of UPGMA cluster analysis and PCoA grouped the eleven date palms according to their geographical location and sex. In addition to classical morphological characters, the current study confirmed the importance of using SCoTs as functionally gene-based multi-loci markers besides nuclear SSR loci to assess the genetic variations and cultivar identification among Egyptian date palm genotypes