A Nymphaea thermarum, the smallest waterlily in the world and extinct in the wild, was taken from the south west London visitor attraction.
A Scotland Yard spokesman said the theft occurred between 8.30am and 2.55pm on Thursday at the Princess of Wales Conservatory.
Experts believe the culprits would have had to dig or pull up the plant from a shallow pond.
Nymphaea thermarum was discovered in 1987 in just one location, Mashyuza in Rwanda. But it disappeared from there around two year ago due to over-exploitation of a hot spring that kept the plants moist and at a constant temperature.
There are more than 50 of the waterlilies at Kew, which is the only place in the world where they are regularly propagated in large numbers.
Their leaves can be as small as 0.4in in diameter.
Anyone with information regarding the theft is asked to contact police on 020 8721 5934.
Richard Barley, director of horticulture at Kew Gardens, said: "Our staff are dedicated to the conservation of plants and 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."