This study attempts to carry out a critical revision for the genus Ephedra in Egypt based on morphological characters for leaf, stem and flower. DNA sequencing data used for the first time for DNA barcoding of the family Ephedraceae in Egypt. One chloroplast marker -intergenic spacer trn-H/psb-A and another nuclear Internal Transcribed Spacer (ITS) were sequenced to authenticate the identification and to reconstruct the phylogenetic relationships of the Egyptian Ephedra species. The results revealed that, the name of Ephedra ciliata Fischer & C. A. Mey. was illegitimate and became a synonym to Ephedra foliata Boiss., which reported here as accepted name. The current work recommends using the DNA barcode as a tool for species identification of Ephedra species as well as other gymnosperms in Egypt.