There have been gardens and parkland on the present site since at least the late 17th Century. Gordon's 1647 map of Old Aberdeen shows 'Clunys Garden' lying between the then Old Aberdeen Loch and St Machar's Kirk.

'Abredoniae novae et veteris descriptio'. Surveyed by James Gordon in 1647

The modern Garden dates from 1898, when Miss Anne Cruickshank bought the buildings and playing fields of The Old Aberdeen Gymnasium, a private school for boys, and presented them to the University to establish a Botanic Garden. The original imposing granite school building, now part of the School of Biological Sciences, is on the right as you enter the Garden from The Chanonry. Soon afterwards, the strip of land alongside what is now St Machar Drive was added, including land which had been the first Aberdeen Football Club pitch, and a market garden, whose owner became the first Head Gardener. A few years later the land immediately to the north, comprising No 8 The Chanonry and its large garden were added. The house at No 8 The Chanonry was thereafter home to successive Regius Professors of Botany until it was sold in the 1980s. Finally in 1966 the land still further towards the River Don, in the angle between The Chanonry and Tillydrone Road became available, and this allowed the development of an arboretum.

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