The ancestor of the Jardin des Plantes et de la Nature is the sacred grove of the kingdom of Porto-Novo. In 1895, part of the forest was changed into a botanical garden by the French governor of the colony of Dahomey, whose residence was alongside the grove. In 1905, it contained 630 species of trees over a surface area of 6,30 hectares divided into Garden 1, Garden 2 and Garden 3.
After independence, the decline of the garden began. The extension of the administrative buildings led to the reduction of Gardens 2 and 3, and to the total disappearance of Garden 1. Lack of maintenance aggravated the loss of biological diversity of the garden, which had become an inhospitable wasteland, containing only 300 species in 1998.
It was in order to end this decline that the garden was put under EPA management in 1998 by the Benin Ministry of Agriculture with a view to opening it to the public.