The Nothofagus gunnii, one of the few of its kind in the UK and only planted in Britain after years of negotiations by botanists, was pulled from the soil of the Royal Botanic Gardens in Wakehurst Place, West Sussex.
The theft comes after the conservation charity English Nature and the Association of Chief Police Officers announced a drive to tackle theft of rare plants which are stolen from nature reserves and wildlife parks before being sold on the black market.
The five-year-old southern beech tree is revered in Tasmania because of the vivid colours that its leaves turn. The severing of roots of the sapling means that even if it were to be discovered, it would not be able to be revived, according to Andy Jackson, the head of Wakehurst Place, who travelled to Tasmania to collect the seedlings in 2000 after spending 11 years in negotiations.
" It is the botanical equivalent of stealing rare jewels", he said. "It was the culmination of nearly 15 years work, so it is pretty gut-wrenching".
The sapling, which was developing the distinctive corrugated style leaves, was creating some excitement amongst botanists and scientists, some of who were among a group to be shown the rare sapling, when the theft was discovered last Wednesday.
Security has been heightened on the 500 acre-estate since the theft, which Mr Jackson believes was most probably carried out by an "obsessive type" fixed on owning the 2ft tree, which would have grown to 7ft.