The Scottish Government has designated flame shell beds in Loch Carron, Wester Ross, as a Marine Protected Area.
An urgent Marine Conservation Order has been put in place banning mobile gear fisheries, such as dredgers, from the area, initially for one year.
Following an investigation into claims the beds had been damaged by scallop dredging, an inquiry found the damage to the reef was consistent with this type of fishing which was legal there before the ban.
The investigation also found it is possible for the damaged beds to recover as part had survived and another nearby bed remained intact.
Flame shells - bivalve molluscs with a fringe of orange tentacles - build nests from shells, stones and other materials, and live completely hidden inside them on the seabed.
Hundreds of nests can combine to make a dense bed, which supports myriad other species, including young fish and scallop spat.
Environment Secretary Roseanna Cunningham said: “We take our duty to protect Scotland’s rich marine environment extremely seriously and recognise the importance of safeguarding vulnerable habitats like flame shell beds.
“By introducing a Marine Protected Area and putting in place a ban on dredging we hope to ensure the recovery of the flame shell beds in Loch Carron.
“While we recognise there are concerns around scallop dredging in coastal waters, we must balance environmental concerns with the need for legitimate and sustainable fishing.
“The Scottish Government will now begin work immediately to identify if there are other areas which should be protected.”
Conservation charity WWF Scotland welcomed the move to prevent further damage to the seabed.
The charity’s acting director Sam Gardner said: “This recent incident clearly shows the importance of completing the Marine Protected Area network and ensuring the jewels of Scotland’s seas are there for future generations to enjoy.”