The groundwork for a botanical garden was formed by Alexandar Moon in 1821. He used the garden for coffee and cinnamon plants. The Botanical Garden at Peradeniya was formally established in 1843 with plants brought from Kew Garden, Slave Island, Colombo and the Kalutara Garden in Kalutara. The Royal Botanic Garden Peradeniya was made more independent and expanded under George Gardner as superintendent in 1844. On his death in 1849 George Henry Kendrick Thwaites became superintendent. He served until 1879` when he was succeeded by Henry Trimen who served until 1895.
The garden came under the administration of the Department of Agriculture when it was established in 1912.
There are avenues in the river drive such as Cook`s Pine Avenue, Palmyra Palm Avenue, Double Coconut Avenue, Cabbage Avenue and Royal Palm Avenue. The classical Avenue of Palms is in this Garden. One item with a significant history is the Cannonball Tree planted by King George V of the United Kingdom and Queen Mary in 1901. It is often laden with fruit which are thought to resemble cannonballs.
During World War II, the the Botanical Garden was used by Lord Louis Mountbatte, the supreme commander of the allied forces in the South Asia as the headquarters of the South East Asia Command.