For many of us, the pygmy Rwandan waterlily might not look like much, pretty though it is. The smallest waterlily in the world, its flowers are barely 2cm across, its pads often even smaller. But somebody knew what they were looking for. On Thursday, the plant, Nymphaea thermarum, which was discovered in a single location in Rwanda in 1987, was taken from a conservatory at the Royal Botanic Gardens in Kew during its opening hours.

In a statement, Richard Barley, director of horticulture at Kew, said: "When incidents of this nature occur, it is a blow to morale. We take theft of our invaluable scientific collection of plants very seriously and this matter is with the Metropolitan police." The value, Barley added, "is very difficult to determine. It is a critically endangered plant and Kew is one of only two places in the world that propagate it, with a very small number left in the wild."

The theft of this plant could be part of a global illegal wildlife trade. Anastasiya Timoshyna, medicinal plants programme leader for the Traffic network, which monitors wildlife trade, says the global legal trade in ornamental plants is valued at more than £9bn. The scale of the illegal trade is difficult to estimate, "but we think it is quite high. In 2011, about 6% of all wildlife seizures [which includes rare animals such as reptiles, as well as ivory, and animal parts] made in the EU were of live plants, destined for collections." The most sought-after species are rare orchids and cacti, "which often fetch high prices. A lot of plants are cultivated, but for a collector something rare that comes from the wild will have an especially large value."

In the UK, the endangered Lady's Slipper orchid has a long history of attracting collectors to its yellow and purple blooms. Victorian orchid fanciers, in an obsession known as "orchidelirium", drove it to extinction, declared in 1917. In the 1930s, a single plant was rediscovered and in the decades since its existence has been protected by a tight ring of secrecy, known only to a handful of people who make up the almost equally elusive Cypripedium Committee. In the 80s, scientists worked out how to propagate the orchid from its seeds and it is now grown in other sites in northern England, mostly kept secret, since cuttings are thought to be worth £5,000 on the black market.

But some sites are known - and targeted. In 2009, thieves took part of a Lady's Slipper from the grounds of a Lancashire golf club. Five years earlier, nearly all of the plant was dug up, but luckily some of its roots were left intact. In 2008, rare Dark Red Helleborine orchids were takenfrom an area of the Peak District, one of only five places in the UK where it grows.

Criminals are well aware of the value of the plants they are targeting, says Timoshyna. She believes there have been "examples where as soon as plants are listed as 'threatened' on Cites (Convention on International Trade in Endangered Species) database, their black market prices go up. Traders will wait to see whether it is being listed or not. They hunt for specific rare species." Which can be a disaster for the plants in the wild - luckily, Kew still has around 29 of its waterlilies on display, and another 100 in its nurseries.