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Governor Gipps having approved the establishment of a "public domain for the purpose of rearing and cultivating indigenous and exotic plants", William Londsdale, the Police Magistrate, in 1841 ordered Robert Hoddle, then surveyor-in-charge, to mark out a block of 50 acres on Batman's Hill and the adjoining riverbank. Nothing came of this order, but several other sites were suggested and in 1845 [Superintendent] La Trobe chose the slopes of a gully leading down to the Yarra River near the grounds of Government House. Here John Arthur, [appointed in 1846 as the first Curator of the gardens], fenced a 5-acre paddock and laid it out in flower-beds and plantations. Both he (1846-49) and John Dallachy (1849-57) paid attention to the introduction of exotic plants and permitted the gardens to be used for horticultural shows.(Australian Encyclopaedia, Vol.II, pp.57-58).
In 1857 Ferdinand Mueller, who had been Government Botanist since January 1853, was appointed to the new office of Director of the Gardens. He established close relations with similar institutions throughout the world and effected important exchanges of plants, re-arranged and extended the grounds and paid particular attention to the native vegetation. He also devoted part of the area to plant-beds showing a scientific arrangement of plants in their natural orders and established a national herbarium. (Australian Encyclopaedia, Vol.II, pp.57-58).
"Mueller's view of a botanic garden was as a scientific and educational institution and his development of the garden reflected this conviction" (Annual Report Royal Botanic Gardens Melbourne, 1993, p.5)
In 1873 the positions of Director of the Gardens and Government Botanist were divided and Mueller was deprived of the former office. The directorship passed to William Robert Guilfoyle, who during his long term (1873-1909) extended the gardens by over 30 acres and increased the number of species represented. The deepening and straightening of the course of the Yarra allowed an extension of the garden area, taking in the old river-channel and adding it to the existing lake. (Australian Encyclopaedia, Vol.II, pp.57-58).
With his radically different concept of a botanic garden as a place to provide inspiring views and to display plants artistically and influenced by English landscape design, Guilfoyle totally redesigned the Botanic Gardens." (Annual Report Royal Botanic Gardens Melbourne, 1993, p.5)
In 1924 the offices of Director and Government Botanist were again united and the National Herbarium of Victoria was again brought into association with the Gardens, having been separated since Mueller's removal from the directorship in 1873.
The Cranbourne Botanic Garden was initiated in 1970 with the purchase of land by the Government for the purpose of establishing a native botanic garden. Cranbourne was opened to the public in 1991.
After 146 years of being part of the administration of various government departments, management of the gardens passed to the newly established Royal Botanic Gardens Board (VA 3124) in July 1992 under the provisions of the Royal Botanic Gardens Act 1991.