Flameshell beds, feather stars, the common skate and the ocean quahog will be protected alongside sandeels, a staple food of sea birds and mammals, and the black guillemot.
Approximately 20% of Scotland’s seas are now in marine protected areas (MPAs) and the North East Faroe Shetland Channel is estimated to be the largest MPA in the European Union (EU).
Scotland’s seas are the fourth largest in the EU and support many habitats and species including cold water coral reefs, 22 individual species of whales and dolphins and almost half of the EU’s breeding seabirds.
MPAs are designed to conserve a selection of marine species and habitats, and offer long-term support for the services the seas provide to society.
These 30 new sites will contribute to a network to conserve rare or representative species and habitats, allowing them to remain healthy and productive as well as to recover more sensitive species and habitats to a more natural condition.
Ministers are also considering 14 new areas to protect sea birds and a further four locations to protect basking shark and species of whale and dolphin.
Environment Secretary Richard Lochhead said: “These MPAs will help protect and enhance our marine environment so that it remains a prized asset for future generations.
“Our waters support a huge diversity of marine life and habitats, with around 6,500 species of plants and animals, and are among the richest in Europe for marine mammals.
“Many of these sites will provide protections for our seabirds like the black guillemot and sandeels, which provide a vital food source.”
Calum Duncan, convenor of Scottish Environment LINK’s marine taskforce, said: “This is a landmark decision for Scotland’s emerging marine protected area network.
“After many years of unchecked decline, we have now started to recognise that our nationally important sealife and neglected marine habitats need better protection. If well-managed, these MPAs will also work for the public interest.
“They will help to recover our damaged seas and benefit everyone who depends upon their health.
“This is one of the most significant decisions Scottish ministers will ever make and we trust that political commitment will last until we achieve true recovery of our seas.”
Stuart Housden, director of RSPB Scotland, said the announcement is “an important first step” in its campaign for better protection of seabirds.
Where possible, the MPA management will also allow sustainable use of the sea by marine users including the fishing industry.
Bertie Armstrong, Scottish Fishermen’s Federation chief executive, said: “We are pleased that our fishermen have had the opportunity to use their knowledge and experience of our seas to help influence the designation of the final chosen sites.
“We have demonstrated our support already by introducing with immediate effect our own voluntary protection measures in 11 specific sites covered by the new designated MPA network.”
Alistair Sinclair, chairman of the Scottish Creel Fisherman’s Federation, said: “If the whole industry embraces MPAs we will without doubt start the process of enhancing our marine environment, creating more opportunities for communities around our coastline.”
Lang Banks, director of WWF Scotland said: “The next step is to ensure that this network of MPAs are well managed and result in the recovery of our ecosystems for the benefit of all.
“This is a great step towards delivering a marine environment where economic interests can operate in a way that does not have to undermine the health of our seas.”
Alex Kinninmonth, Scottish Wildlife Trust living seas policy officer, said: “This is a huge leap forward for nature conservation in Scotland.
“After many years of making a compelling case for better management of our seas, we are delighted to see these ambitious plans for marine protection.
“Each new MPA forms an important piece of a complex jigsaw that when complete will help turn the fortunes of our sea around.”
Sarah Dolman, North Atlantic programme manager for Whale and Dolphin Conservation, said: “Having provided the evidence and demonstrated huge public support for protection of important whale, dolphin and porpoise habitat, it’s great news that minke whales and Risso’s dolphins are included in the Scottish MPA network.”
Richard Luxmoore, head of nature conservation, National Trust for Scotland, said: “Many of these MPAs - such as South Arran and Wester Ross - have been the direct result of local campaigning and research.
“We know that these measures to recover our sealife have popular support within many communities but there is still work to do.
“Other communities - such as the tireless campaigners of Fair Isle - are still calling for better protection of their local marine environment and we hope that these MPAs mark a new, regionally-sensitive approach to coastal and marine management.”