The wild Carneddau ponies of Snowdonia are a unique breed that need to be protected, say scientists.
A study of their DNA shows they have been isolated for at least several hundred years, according to researchers at Aberystwyth University.
They conducted the first research into the genetic characteristics of the wild ponies, which take their name from the Carneddau Mountains.
Hair samples were taken from different breeds, including Highland ponies.
The aim was to establish to what extent the Carneddau ponies are related to other UK native breeds.
Scientists at the university's Institute of Biological, Environmental and Rural Sciences (Ibers) particularly want to establish whether the ponies were relatively recently separated from the similar Welsh Section A pony.
This is a registered breed that is geographically nearest and similar in appearance to the Carneddau pony.
Clare Winton, an Ibers post-graduate student who performed the study as part of her PhD thesis, said the Carneddau ponies are a genetically distinct population.
"Although the Carneddau ponies have shared ancestry with the Welsh Section A pony, they exhibit genetic signatures demonstrating that the population has been isolated for at least several hundred years," she said.
The results of the findings come after a large number of ponies died during the recent heavy snowfall which hit the hill communities hard.
Hair samples were collected from Carneddau ponies during their autumn round up.
DNA was extracted from the hair and then tested.
Dr Debbie Nash, lecturer in equine and animal science and one of the Ibers researchers, explained that the Carneddau ponies play a vital role within the mountain ecology of the Snowdonia National Park.
But she said their existence was threatened by financial pressure such as costs associated with the legal requirement to passport and microchip every horse in the UK.
"Populations deemed 'rare' receive special exemption from the need for passports and microchips whilst remaining free-living," she said.
However, the Welsh government has allowed a derogation for ponies in the care of the Carneddau Mountain Pony Association.