The law also affects ponies in the Brecon Beacons
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A hundred wild ponies, which were threatened by an EU rule, have been saved by bird charity, the RSPB.
The new law, to protect human health in countries where horsemeat is eaten, means Welsh Mountain Ponies will need £75 passports.
But the Carneddau ponies, which roam the Snowdonia uplands, are worth just a few pounds, so farmers have found keeping them unaffordable.
Now the RSPB has given 100 ponies a home at its Lake Vyrnwy nature reserve.
Mike Walker, manager of the reserve, said: "It was quite fortuitous.
"We had been looking to increase the herd and the CCW (Countryside Council for Wales) gave me a ring and said that there was a big sale coming up, so we went along and bought some."
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I think the ponies are feeling quite at home
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Mr Walker said the hardy ponies were ideal for maintaining the habitat for birds at Lake Vyrnwy.
"The RSPB tends to go for the management of the habitat.
"If you get that right then the birds will follow, so ponies are going to be a vital part in that story."
The RSPB has split its ponies into two herds, with one being turned loose in a 500-acre area and the other in a 2,500-acre area.
"They seem to be settling in very well. I think they're feeling quite at home," said Mr Walker.
The plight of the 300 to 400 Carneddau ponies was highlighted by the Snowdonia Society, which said they were an important part of Wales' culture.
The society wanted to make the animals exempt from the EU rule like Dartmoor and New Forest ponies in England.
But an assembly government spokeswoman said a similar relaxation was not considered viable within Wales.
That is because the hills and commons on which Welsh ponies graze do not have clearly defined boundaries and are not managed by a single body.
The spokeswoman said the final decision about the ponies' future would be made by the EU.