The island of Oronsay and the southern part of neighbouring Colonsay are to be designated special protection areas for hen harrier, chough and corncrake.
The islands and the Renfrewshire Heights moorland overlooking the Clyde are one of two new Special Protection Areas (SPA) designated in Scotland.
The move brings the total number of protected areas to 144.
RSPB Scotland applauded the decision, which it said would protect the habitats for years to come.
The decision to create the SPA's followed consultation by Scottish Natural Heritage with local owners and occupiers on behalf of the Scottish Government.
The status means the rare birds that live there will be given the highest level of protection under European law.
Stuart Housden, director of RSPB Scotland, said: "This is a very welcome addition to the network of internationally protected sites recognised for their rare habitats and the birds and wildlife that they support.
"It will provide significant extra protection for choughs, corncrakes and hen harriers - all of which have suffered long-term population declines and loss of range, not only in the UK but in many parts of Western Europe.
"The challenge now is to make sure that land managers get the necessary support to guarantee that the sites are preserved, and this must include assistance for extensive cattle and sheep systems, which work together to provide both food and habitat for these birds."
The RSPB already manages Oronsay, in the Inner Hebrides, as a nature reserve, where the public can see these rare species of birds as well as other wildlife.