The genus Silene L. is one of the largest genera in Caryophyllaceae, and is distributed in the Northern Hemisphere and South America. The endemic species Silene leucophylla and the near-endemic S. schimperiana are native to the Sinai Peninsula, Egypt. They have reduced population size and are endangered on national and international scales. These two species have typically been disregarded in most studies of the genus Silene. This research integrates the Scanning Electron Microscope (SEM), species micromorphology, and the phylogenetic analysis of four DNA markers: ITS, matK, rbcL and psb-A/trn-H. Trichomes were observed on the stem of Silene leucophylla, while the S. schimperiana has a glabrous stem. Irregular epicuticle platelets with sinuate margin were found in S. schimperiana. Oblong, bone-shaped, and irregularly arranged epidermal cells were present on the leaf of S. leucophylla, while Silene schimperiana leaf has “tetra-, penta-, hexa-, and polygonal” epidermal cells. Silene leucophylla and S. schimperiana have amphistomatic stomata. The Bayesian phylogenetic analysis of each marker individually or in combination represented the first phylogenetic study to reveal the generic and sectional classification of S. leucophylla and S. schimperiana. Two Silene complexes are proposed based on morphological and phylogenetic data. The Leucophylla complex was allied to section Siphonomorpha and the Schimperiana complex was related to section Sclerocalycinae. However, these two complexes need further investigation and more exhaustive sampling to infer their complex phylogenetic relationships.