Begonia elachista was discovered at the mouth of a limestone cave in a national park in central Peru.
The park authorities want to build a tourist route to the cave - a move which could threaten the species.
Staff at the botanic garden hope their work will inform conservation efforts for the new species which has been classed as critically endangered.
The Peruvian cave is the only place botanists know that the begonia grows in the wild, but the Royal Botanic Garden Edinburgh (RBGE) said it was "not a safe haven" for the plant as more tourists begin to arrive
RBGE staff are now working with partners in Peru and the US to try to save it.
Peter Moonlight, a tropical biodiversity research scientist at the RBGE, said the begonia did not deserve its reputation as being "repulsively ugly" - as Monty Don once labelled them.
"Many are still poorly understood although they play a critical role in tropical ecosystems and are of great importance as environmental indicator species," he said.
"In many cases they also have a strong role to play in the horticultural sector and as a food source, medicine or other products of benefit.
"The species discovery programme at RBGE gives previous hidden gems - including begonia elachista - a voice on the global conservation stage."

A study for South Lakeland District Council examined details, including types of wagons, the lengths of routes, and the width of streets.
It also took into account how many right turns vehicles made, as these cause them to be delayed at junctions.
The council said the Â£35,000 cost of the research would be offset by savings of Â£40,000 a year.
Changes, which include different collection days for 65% of households, will come into effect in the autumn.

Crane driver Dempsey Nibbs killed his partner of 30 years after he suspected her of having affairs, the court heard.
Judith Nibbs, 60, described as "bubbly and happy", had predicted her own death, telling colleagues, "If I'm not in on Friday, I might be dead", jurors were told.
Mr Nibbs, 69, of the Charles Estate in Hoxton, denies murder.
The court heard that Mr Nibbs carried out the act because he thought his partner was a "snake", and said he had killed her while "defending himself".
Crispin Aylett QC, prosecuting, said the couple's relationship had soured in the spring of 2014 as Mr Nibbs suspected his partner of infidelity.
Ms Nibbs had confided in her sister and a colleague at Meals on Wheels that her partner had threatened to kill her and grabbed her by the throat.
During a row on 7 April, she had taunted Mr Nibbs with details of her infidelities, saying: "I have had sex eight times."
On the night of 10 April, Mr Nibbs attacked her in their Hoxton flat and knocked her out, Mr Aylett said.
"Having attacked his wife, the defendant then took up a kitchen knife and cut off her head," he said.
The court heard how Mr Nibbs disposed of remains down the lavatory, before writing a suicide note to his son and ringing police to tell them they would find "a couple of dead bodies" at his home.
The trial heard that Mr Nibbs shown no signs of mental illness in the wake of the killing.
Ms Nibbs's former workmates described her as a happy, joyful, bubbly and open-minded woman.
The trial continues.
The newest and smallest species of begonia ever found has begun to flower at Edinburgh's Royal Botanic Garden.
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Bin collections in south Cumbria are due to change following a project to "optimise" collection rounds.
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A jealous man beheaded the mother of his two children in an act of "pure hatred", the Old Bailey heard.