A total of 30 new MPAs have been designated, encompassing areas that are home to flameshell beds, feather stars, the common skate, the ocean quahog, sand eels, and the black guillemot.
Scotland's seas are the fourth largest in the European Union 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.
The protected areas 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. The North East Faroe Shetland Channel is now estimated to be the largest MPA in the EU.
Scottish Government 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 areas will help protect and enhance our marine environment so it remains a prized asset for future generations. Our waters support a huge diversity of marine life and habitats, with about 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 sand eels, which provide a vital food source."
Calum Duncan, convenor of Scottish Environment Link's marine taskforce, said: "After many years of unchecked decline, we have now started to recognise our nationally important sealife and neglected marine habitats need better protection. If well-managed, these Marine Protected Areas will also work for the public interest.
"They will help to recover our damaged seas and benefit everyone who depends upon their health."
Where possible, the MPA management will allow sustainable use of the sea by marine users, including the fishing industry.
Alistair Sinclair, chairman of the Scottish Creel Fishermen'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."
The new sites are in addition to the Special Protection Areas for seabirds such as puffins and kittiwakes, Special Areas Of Conservation for bottlenose dolphins, coral reefs and seals, and Sites Of Special Scientific Interest, which protect a range of coastal habitats and species, including seabirds, seals, sea caves and rocky shores.
The Government said the addition of further MPAs means 20 per cent of Scotland's seas are protected.
Lang Banks, director of WWF Scotland, said: "The next step is to ensure this network of Marine Protected Areas 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."
Richard Luxmoore, head of nature conservation for the 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 these measures to recover our sea life 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 these MPAs mark a new, regionally-sensitive approach to coastal and marine management."
Stuart Housden, director of RSPB Scotland, said the announcement was "an important first step" in its campaign for better protection of seabirds, but he called more protection further out at sea where seabirds feed.
"The Scottish Government must bring forward more Special Protection Areas for seabirds soon and also recognise the value of Marine Protected Areas for other seabirds, such as razorbills, kittiwakes and Arctic terns," he said.