PHLOMIS AUREA Decne. (Lamiaceae), which have future antidiabetic drug yielding potentials, is an endemic species, restricted to the high altitudes in five main habitats in southern Sinai. The genetic characterization of individuals from different populations is necessary to construct proper conservation programs. Thus, the present study was conducted to achieve two main goals; 1) Finding the genetic diversity among Phlomis aurea populations through variation in seed storage proteins electrophoretic pattern and Inter Simple Sequence Repeats (ISSR) finger printing as a dominant DNA molecular marker. 2) Perceive the relationship among these biochemical and molecular parameters with the different habitats in Saint Katherine Protectorate (SKP) are in South Sinai. Mature dry seeds from 30 individuals representing different populations were used for protein analysis using SDS-PAGE technique, 12 individuals of them were chosen for ISSR analysis. The former test produced 20 protein bands, three of them were common to all plants (species specific) and could be used as finger prints for Phlomis aurea. It was suggested that seed storage protein patterns are affected by aspect direction, altitude and slightly affected by habitats. ISSR analysis showed that decreasing genetic variation of Phlomis aurea individuals from different habitats in the following order: Wadibed> Slope> Gorge>Basin. This open area habitat contributes to high percent of hybridization and consequently results in high genetic polymorphism.