Sue Nottingham, editor of Plantlife magazine, said: "It's been a bad year for the beautiful meadow clary, which has been lost from its last site in Wales.
A small Site of Special Scientific Interest (SSSI) in Monmouthshire provided a last haven for meadow clary and other grassland species, including cowslip and greater knapweed.
Dr Trevor Dines, Plantlife Cymru's conservation manager, said that meadow clary had joined two other recent cases of native plants disappearing from Wales.
Dr Dines said that meadow clary is the latest grassland wildflower to fall victim to the intensification of agriculture in post-war Wales.
The meadow clary was first recorded in Wales in 1903 and there was a big population of it in Monmouthshire in the 1950s and 1960s," he said.
What meadow clary doesn't like is no grazing at all.
The management plan drawn up for the site in Wales was based on experience from sites in England, where the meadow clary is now thriving.
In Gloucestershire, there were just 40 plants of meadow clary in 2007 and there were 600 in 2009.
But because meadow clary spreads through bee pollination, we cannot just take seeds from many miles away in England because its genetic make-up would be different as bees can't travel that far.
Once good management is secured for the site, plants will be reintroduced and meadow clary will hopefully flower once more in Wales.