Thieves dug up nearly the whole population of meadow clary (Salvia pratensis) from conservation charity Plantlife's Ranscombe Farm Reserve, in Medway, last week.
The loss of the 12 plants was discovered by the reserve warden last Wednesday and Kent police are investigating.
It is an offence to pick, uproot or damage the plants, which are protected under a 1992 amendment to Schedule 8 of the Wildlife & Countryside Act 1981.
S. pratensis is a perennial from the sage family. It is classified as near-threatened and survives only at 21 locations in the UK.
Plantlife chief executive Victoria Chester said: "The loss of so many meadow clary plants from the small population at the reserve is devastating for the conservation of the species here.
"It is particularly distressing because meadow clary plants have been recorded at this site for more than 200 years. Plantlife had been successful in doubling the number of plants over the past two years through active management of the site, but it may now be difficult for the population to survive the loss of so many plants in one go."
Plantlife chairman Roger Crofts said: "This is a shocking example of environmental vandalism. Meadow clary is a rare and declining species, one of the crown jewels of British flora, so we must stand firm against criminal acts like this."
Detective Sergeant Adam Marshall of Medway Police is urging anyone who may have been offered the plants or who has any information to contact the police.