There are increasing threats facing the rare plants including the endemic populations. Also the potential development of the earth's vast desert areas for agriculture and other human-needs demands an awareness of the ecological characteristics and requirements of desert vegetation. Saint Catherine area has a unique location and environment. The vegetation and wild life in Saint Catherine area is subjected to great disturbance through the unmanaged human activities. In the present study we had used seed ecology in order to contribute in designing a sound long term conservation plan for the threatened endemic studied medicinal species; Hypericum sinaicum, at two levels; (a) soil seed bank and its relationship to above ground vegetation and (b) the germination response at different conditions and pretreatments on wetted substrate. Hypericum sinaicum grows in Sinai on mountainous sheltered moist crevices and in Hijaz in the extreme north-west of Saudi Arabia and in Edom in Jordan. The results revealed that seven endemic species were identified in soil seed bank; Veronica khaiseri, Hypericum sinaicum, Nepeta septemcrenata, Plantago sinaica, Origanum syriacum, Phlomis aurea, and Primula boveana. Germination treatments on Hypericum sinaicum seeds showed that calcium carbonate (CaCO3) and hot water of 50°C treatment was found to be most effective to improve seed germination depending on doses, while other treatments were efficient to a lesser degree. As a general conclusion, the present study clarified that the behaviour of endemic species along environmental gradients varies greatly, as well as in its strategies in struggling for existence.