The "puzzling" fungus was found by a worker at Moelyci Environmental Centre near Bangor as he was collecting specimens for a fungi course.
John Harold had to consult an expert to find out it was Squamanita pearsonii, commonly known as Strathy Strangler.
He was told the species has only been found twice before in Britain.
The last discoveries, in 1950 and 2004, were both in the highlands of Scotland.
"There are so many questions to be answered about this bizarre fungus"
"I feel really privileged to have found this extraordinary species," said Mr Harold.
He is the conservation officer at the community-owned farm, where the Moelyci Environmental Centre is based at Tregarth near Bangor.
Mr Harold added: "I was already fascinated by the beautiful wax cap fungi we have in such diversity here which is the produce of centuries of traditional grazing."
He said that the Moelyci site was lucky to have escaped modern farming methods, building development and even simple neglect.
Further study
With grassland fungi such as wax caps, fairy clubs and earth tongues the farm already had a place on the mycological map in the UK.
"There are so many questions to be answered about this bizarre fungus - it is not even clear which other fungi it parasitizes, nor how it does it," he said.
"And why is it so rare? Hopefully we may get a chance to study it and find out a little more about it," he added.
The 350-acre Moelyci site includes 230 acres of Special Scientific Interest.
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