The two endemic plant species Silene leucophylla and Silene schimperiana (Caryophyllaceae) are native to the Sinai Peninsula which considered as one of the floristically richest phytogeographical hot spot regions of the Mediterranean basin. The acquaintance of Sinai’s biodiversity is crucial for conservation and sustainable development. Endemic plant species of Sinai are vulnerable to anthropogenic threats due to their relatively low population size. The current study reinvestigated the taxonomic status of two medicinally important and vulnerable species. The integrated approach of macro and micro-morphological traits using a scanning electron microscope (SEM) as well as phylogenetic analysis were conducted. Phylogenetic reconstruction using Bayesian Inference based on DNA sequences of nuclear (ITS) and chloroplast (rbcl and matk) markers retrieved the species phylogeny successfully. Silene leucphylla and Silene schimperiana was placed phylogenetically within the whole genus. The sectional classification of the two species was confirmed. Silene leucophylla was placed in section Siphonomorpha while Silene schimperiana allied to section Sclerocalycinae. The current study reassured that the integration between the various morphological and molecular approaches is substantial to identify, determine the taxonomic status, and reveal the phylogenetic position of those two endangered plant taxa.