Bothy owners said they are being forced to lock their doors and charge guests after visitor numbers became 'unsustainable' - with a surge in stag parties and vandalism.
The buildings are typically situated in remote wilderness areas, providing shelter or an overnight stop for walkers on a long-distance trek.
But concerns have been raised they are becoming a 'destination' for partygoers looking for a free night in the wild.
Two bothy owners have now withdrawn from the Mountain Bothies Association, the charity which maintains around 100 of the buildings across the UK.
An Cladach on Islay, Inner Hebrides, and Peanmeanach at Ardnish, Scottish Highlands, will now have to be accessed with a key, with owners charging for an overnight stay.
Owners said their popularity soared following books like The Bothy Bible, with group of up to 30 people gathering for 'free stag parties'.
Peter Stewart-Sandeman, owner of the Ardnish Estate, said online articles advertising lists of bothy locations 'sucked in the wrong type of people'.
He will now charge £50 a night for six people at the weekend and £40 for during the week.
Mr Stewart-Sandeman said: "Visitor numbers at Peanmeanach got unsustainable.
"Sometimes there would be 30 people there and it would be used as a free stag party venue.
"Traditionally, the location of bothies would be passed down word-of-mouth to someone you trusted.
"There are now lists of bothies out there on the internet and books such as The Bothy Bible, which generated a lot of articles.
"Unfortunately, it just sucked in the wrong sort of person.
"I know who is there and I have their bank details, should there be a problem."
David Gillies, manager of Dunlossit Estates on Islay, said a booking system would be introduced at An Cladach from next year, with 50 per cent of proceeds going to MBA.
He said bothies have become free 'destination' breaks for people instead of being used as a shelter for walkers, who would often arrive to find the bothy full.
Mr Gillies said: "The publication of The Bothy Bible came almost at the same time as bothies were appearing in the press as great places to go that didn't cost anything.
"Instead of them being used as a shetler if people were out walking, they started to become more like destinations.
"Sometimes people would arrive, it would be full, and they would have to walk out again.
"It's a three-hour journey on foot. Now we'll know who is there."
Geoff Allan, author of The Bothy Bible, said it was "very, very sad" the bothies had withdrawn from the MBA.
He said: "I have been bothying since the 1980s and I just wanted to share my knowledge - the book was very much written from the heart.
"There are numerous articles about bothies but really I have become a lightning rod for all the negatives, all the anti-social behaviour, all the littering.
"The key element is there is a bothy code. Respect the bothy, respect the landowner, respect the other people you meet.
"Bothies have always been a destination and now this has caught the imagination of more people, not just the Munroists or the hardcore adventurer."
A spokesman for the MBA said it was grateful for the generosity of the two bothy owners and "fully accepted" their decision.
He said a key task of the organisation was to promote responsible use of bothies amid the increased publicity.
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