Although there are perennials almost in all parts of the Botanical Garden, a sufficiently large number come together to form a separate garden in the depression facing the old town wall, created when the old greenhouse was torn down and archaeological excavations were conducted on the site in the 1990s.
The fact that the site is shielded from the winds and receives ample sunshine makes it suitable to many frost-sensitive trees and shrubs rarely used in Estonia in greenery applications, such as Viburnum x bodnantense and Viburnum x rhytidophylloides, Kouse dogwood (Cornus cousa) and Korean mulberry (Morus australis). On the south-facing slope, however, the ginkgo (Ginkgo biloba) and tulip tree (Liriodendron tulipifera), which are already quite large, do very well.
The garden's selection of plants is not based on fixed rules but has evolved following natural garden design principles which give the gardeners a free hand in lending shape and colour to the grounds. The Perennials Garden is dominated by tall species such as Cimicifuga, Ligularia, Miscanthus, Rheum, Acanthus, Stipa and others.
The Perennials Garden has species from East Asia, the Caucasus, North America and South Europe.