The Date Palm (Phoenix dactylifera L), germplasm commonly cultivated in Egypt, shows a wide range of
repining periods and fruit quality and is an unexploited resource for breeding programs. The main purpose of this study
was to fingerprint 45 date palm genotypes and accessions and to construct a molecular database including the cultivars
commonly grown in Egypt. An analysis of thirty three microsatellite simple sequence repeat (SSR) loci out of thirty five
markers was performed to define distinct specific alleles across all loci, genetic similarity within cultivars in each
region of five different locations and possibility of linking morphological traits with molecular data. In general, the
results indicated the possible use of SSR analysis to detect cultivar-specific markers for forty five Date palm cultivars
and accessions under investigation that can be used to discriminate among the cultivars and genotypes. The genetic
distance among populations compared to each other (Hayani, Samany and Zagholol) which presented at different
locations in this study, may or may not correlate with the geographical distance between them in some species,
depending on natural and artificial factors involved in shaping the population genetic structure of the species. Based on
our findings, it is clear that there is some discordance between the data corresponding to molecular variability and those
related to the variability available for breeding purposes (phenotypic variability). However, the use of 33 polymorphic
microsatellite markers to study Egyptian date palm germplasm suggested that this is reliable, efficient and effective
marker system that can be used for diversity analysis, and subsequently in crop improvement programs.