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Travellers to Wales from mainland Portugal and six Greek islands must self-isolate for 14 days from 04:00 BST Friday.
It is the first time the Welsh Government has made its own quarantine changes.
People returning from Gibraltar and French Polynesia will also be required to self-isolate.
Crete, Zakynthos, Mykonos, Lesvos, Paros and Antiparos are among the Greek islands affected.
The announcement comes on the same day the UK government decided not to add Portugal to its quarantine list, despite a rise in cases.
The latest Welsh Government rules apply to travellers arriving home in Wales regardless of what part of the UK they return through - including English airports.
The Portuguese islands of the Azores and Maderia were not included in the announcement.
Travellers to Wales from Zakynthos were asked to self-isolate earlier in the week, but the changes mean those who do not self-isolate now face potential fines.
Greece had not been on the quarantine list, except in Scotland where it was added on Tuesday.
Portugal is expected to be added to Scotland's list from this weekend.
Wales' Health Minister Vaughan Gething said he had taken the decision because of a large number of cases of coronavirus "imported into Wales from tourists returning from the Greek islands".
He said there were more than 20 cases confirmed in passengers on one flight from Zante to Cardiff.
The UK government's Transport Secretary Grant Shapps ruled out any similar changes in England on Thursday.
Under current rules, breaking the quarantine restriction could result in a fine of £1,000.
Travellers abroad are expected to fill in a form online with their contact details 48 hours before they arrive back in the UK. Not providing accurate details could also result in fines of £1,920.
Because it is a public health measure, the quarantine system is set by the Welsh Government.
Up until now, Wales has followed the UK government in deciding which countries travellers could return from and not need to self-isolate.
It has also followed the changes made to that system, including the recent decision to order travellers from Switzerland to self-isolate.
Analysis by Ione Wells, BBC Wales Westminster correspondent
Wales, for the first time, has now announced significantly different quarantine rules to those across the border.
The Welsh health minister says this action came after "clear advice" from the UK's Joint Biosecurity Centre (JBC) that travel from these countries poses a public health risk.
But the UK government's Transport Secretary Grant Shapps also cited the JBC when announcing there was no need for additions or removals to the travel corridor list for England today.
These differences come with complications.
With only one major airport in Wales - Cardiff - many passengers flying into places like Bristol or Birmingham will land into one set of rules but face another when they get home.
Are you affected by the new quarantine rules? Tell us about your experience by emailing haveyoursay@bbc.co.uk.
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