One of the Botanical GardenGarden's primary aims is to protect rare and endangered plants that are native to Israel. Accelerated urban development, decreased water resources and the penetration of invasive plant species is leading to the destruction of natural habitats, the displacement of local flora and a rise in the number of endangered plant species. The Mount Scopus Botanical Garden displays close to 1,000 species of native Israeli plants, of which approximately 240 are considered rare or endangered.

The Geophyte Collection - Bulb plants and buds of various types. This collection includes the endemic Oncocyclus Iris.

The Seed Collection - Established in order to enrich the Garden's plant collection, to enable trade with other botanical gardens, and as a possible seed reserve for the reintroduction of wild species.

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