The Botanical Garden of the University of Tartu was founded in 1803, near what is now the Vanemuine Old Theatre House. In 1806 the garden was relocated to more suitable site, on the ruins of the ancient city wall and fortifications near  the river and ponds. 

The department of Plant Taxonomy was founded on the current site, in front of the greenhouses, as early as in the year 1870.

The area for growing monocots was re-designed into a free-shaped one at the beginning of the 1990s,. The most rich-in-species groupings comprise the family Liliaceae (genera Tulipa, Allium, Fritillaria, Ornithogalum); the Iris family, the Orchid family, families Gramineae, Cyperaceae, Araceae. There are more than 300 species of monocotyledonous plants growing in the area. The plants are situated to the right of the main entrance, according to their plant geographical distribution. The species from Europe and Asia Minor have been planted alongside the pathway, the plants of Eastern Asia are growing at the tropical greenhouse, the plants from Africa and South-America are in the warmest habitat – the bottom of the hollow. Spring-time flowering starts already in March by a number of bulbous irises, crocuses, snowdrops. They are followed by squills, tulips, fritillarias, tuberous irises. Some of the bulbous plants flowering in early spring have been planted to decorate the shores of the great pond, together with day lilies. The Eremurus are undoubtedly  the most eye-catching plants in the department, the highest of them Foxtail Lily has grown in the Garden for decades and reproduces by self-propagation.The orchids are represented by 10 domestic species, the most decorative of them is Cypripedium calceolus.
The area for dicots has been in the same place since the foundation of the relevant department. The current layout of the beds, based on the system created by A. Engler, has been maintained here since 1909. The more primitive families are planted near the gates, the imaginary development line goes along the wall towards the big larch and then, in a U-shape manner back to the path, along the Palm House. A total of 800 natural species grow in this area. The herbaceous perennials constitute the majority of them (more then 60%), but there are also annual plants and those surviving the winter. The most rich-in-species is the Compositae family with 180 species. The department introduces different types of stems, leaves, flowers, inflorescences and fruits. The Berry Catchfly (Cucubalus baccifer)with a lying stalk is an example of an unlikely stem type; the peculiar lamina is represented in the Yellow Vetchling (Lathyrus aphaca) with tendrils etc. The decorations of the department are a pool and some granite statues.

The Park is located on the top and slopes of the former bastion and covers the biggest area in the Garden. The arboretum contains species of woody plants from different temperate regions of the world. The area of East-Asian woody plants begins immediately behind the greenhouses. Abundant ground vegetation comprises beautifully flowering rhododendrons, maples with varying foliage and yews with deep-green thorns. The trees and shrubs from Europe are growing on the banks of the ancient bastion. The woody plants of North America are on the northern bank of the former bastion, in the rear and the northernmost part of the garden.

The perennials grow in the department of plant taxonomy, in the rock garden and the arboretum. The plant taxonomy and geography of the relevant departments has been followed when planting the perennials. The prevailingly high-growing perennials in the valley in front of the old town wall form a separate garden. This garden was designed on the site of the former greenhouse for tropical plants and cacti. The plants from the Caucasus have been planted on the western slope. The East-Asian plants grow from here down to the bottom of the valley. The perennials of South-European origin grow on the warmer western slope. Behind the city wall, there is the collection of iris cultivars, with more than 60 varieties. And a new department of peonies – 250 varieties is situated behind the pond

The clematis garden was built in 2006 and is situated right from the entrance from Emajõe St. In this department we
present only native cultivars of clematises, by breeders Uno Kivistik and Eino Kala. The flowers of these hybrids develop on the same-year growouts and they flower from the end of July till first colds. The color of the flowers of these varieties vary from white to deep red.

The annuals collection varies from year to year, but the average number of taxa is 100 every year. There are two fixed places for exhibiting annuals, first besides the Palm House and second one in the rock garden on a sunny slope where annuals are planted to form a picture.

The department of alpine plants is located in the middle of the garden, on the slopes and the valley of the former St. George’s Bastion of the town wall. The plants are selected according to their natural habitats – the upper part of the forest zone of mountainous regions and the alpine zone. The site was founded approximately a century ago, on the initiative of Professor Nikolai Kuznetsov. Currently 900 taxa of alpine plants grow in the Rock Garden. The short vegetation period of Alpine conditions, extreme temperature fluctuations, intensive sunlight, strong and dry winds enable the growth of cushion or mat-like plant forms with low rosettes. Their roots are long and forge into deep, more moist and cooler layers of soil. The leaves are compressed near the stems, small, leathery or fleshy and often covered with hair. Alpine plants are rich in blossoms. The flowers are large and colorful, so as to better attract pollinating insects.
The other part of this department is the talus garden which reaches the shady slope and is also the site of the turf garden. The ascent, moulded from peat loaves is suitable for plants growing in acid soils. In 2002, a summer stage for concerts, exhibitions and presentations was erected in the northern part of the Rock Garden, replacing the old greenhouse.

The Rose Garden is located near the  river-side edge. In July, during the blooming time of the roses, the garden offers a pleasant experience with its bright colors and unique world of fragrances. The Rose garden was thoroughly reconstructed in 1988-1989, the collection was renewed in 1997 and 1999, primarily with regard to varieties. The more than 200-cultivar collection of roses provides an overview of the most important modern variety groupings of cultivated roses, their decorative character and suitability to be grown on an open field. The groups of Floribunda roses (strong and well-forking stems, dense foliage, bloom bounteously) and Hybrid Tea Roses (long few-branching stems and large colorful blossoms) are represented most abundantly

The Department of Estonian Plants is located in the western side of the Botanical Garden, beside the Department of Plant Taxonomy. This department was founded by Professor
F. Bucholtz during 1919-1923. In an unorganized manner, the plants of Estonia have existed in the garden since the early days. Spring comes to the department when the poisonous mezereon (Daphne mezereum) bursts into blossoms. Various fern plants remain in the shady part, common polypody (Polypodium vulgare), bracken fern (Pteridium aquilinum). Protected species, being rare in Estonia is the star gentian (Swertia perennis) and the most well known native orchid ladu’s slipper (Cypripedium calceolus)

The Palm House, built in 1982 has the height of 22 meters and the floor area of 500 m2. There are 58 species of palm trees originating from America, Africa, Asia and Europe. The highest palm is the California fan palm (Washingtonia filifera) and the oldest palm is Canary date palm (Phoenix canariensis) – 90 years.  There is gorgeous liana bougainvillea (Bougainvillea glabra) climbing along the balcony. On the hot sunny side of the balcony we can find succulent plants. In the middle of the house an epiphyte tree is exposed – a trunk with bromeliads and cacti displaying a typical rainforest habitat. Under the bananas there is a pool with fish and tortoises.

The subtropical house displays plants of subtropics from all over the world. First two beds consist of plants from Australia – the most common representative is eucalyptus, which in Australia grow into enormous trees and with acacia build up 95% of native dendroflora. The ground-covering plant here is Viola hederacea. The big fir-like tree is Araucaria cunninghami from the Mediterranean region. The representative of Africa is Harpephyllum caffrum. The tree with the syringa-like blossoms is Melia azedarach from East-Asia. American plants are represented with Juanulloa mexicana from genus Solanacea.

In the tropical house the main goal is to expose the representatives from tropical America. Some of them are grown from seeds and seedlings brought directly from expeditions. The tropical climate zone has no seasons and the changes in the amount of rainfall and temperature are minimal. We expose tropical epiphytes – bromelias and orchids, lianas and trees. Among the best-accommodated plants are begonias and Heliconia psittacorum – taken to our garden from the expedition to French Guajana in 2006. The most remarkable wooden plants are Bauhinia forficata and the representatives of Myroxylon.

The collection of succulents introduces plants that have become adapted to life in dry climate, bright sunlight and strong winds. In order to survive plants have their means of protection – a strong covering or cuticula, wax layer, hairs and spikes, deep ribs. Leaves can be thick and coriaceous, or indeed transformed into hair.  The stem has become the tissue that preserves and assimilates water. The homes of such plants, with minor exceptions, are Africa and Central and South America. The collection on 100 m2 consists of 600 taxa. The African cactuses are the following – Aloe, Aeonium, Crassula, Euphorbiaceae. The representatives of the New World are Cactacea, Agavaceae. The oldest plants here are the 80-year old Golden barrel cacti (Echinocactus grusonii). The succulents from the genera Allaudia and Pachypodium, originating from Madagascar, have a peculiar exterior.