The Botanical Garden is a municipal organisation founded in 1972 thanks to two principle promoters, the engineer in charge of Gardens for the city, Luciano Malanchini, and Guido Isnenghi, an agriculturist and lover of local flora with an artistic eye. Both of them contributed to the promotion of the International Association of Alpine Botanic Gardens (Associazione Internazionale Giardini Botanici Alpini - A.I.G.B.A.) of which the Bergamo Gardens was Head Office for several years.
The original setting presented innovative ideas as it endeavoured to reconstruct the natural habitat of the local flora, underlining its original name ‘Giardino Botanico Bergomense' and its reference to Lorenzo Rota (1855 - 1918), the first chronicler of the flora of the Province of Bergamo. Alpine species were particularly favoured, both chalk and acid types and for several years the Botanical Gardens were considered almost exclusively an alpine botanical gardens.
Between 1983 and 1987 it suffered a period of managerial problems and an absence of personnel with botanical experience so it was closed to the public. In 1989 scientific collaboration began with the Civic Museum for Natural Science and their botanic environmentalist resulting in the re-establishment of the Gardens' importance and scientific coherence as a showplace.
For about ten years the Gardens were an integral part of the Museum. The revival took place thanks to a re-organisation of the presentation, the organisation of temporary exhibitions, the coordination of promotional activities and guided visits, the introduction of scientific studies and programmes for the reintroduction of endangered plants as well as the involvement of mass media.
Since 1999 the Botanical Gardens have had their own Director and, after an initial re-organisation, it became a separate municipal museum recognised by the Lombardy Region in 2004.
The Gardens have grown both in prestige and in activities, visitors have increased progressively from 2,439 in 1991 to over 16,000 in 2005. Various hypotheses for future development which include expanding the Gardens or the creation of larger Botanical Gardens are still being considered.